Starting phenix.real_space_refine on Sun Mar 10 22:07:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpe_16780/03_2024/8cpe_16780.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpe_16780/03_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_16780/03_2024/8cpe_16780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpe_16780/03_2024/8cpe_16780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpe_16780/03_2024/8cpe_16780.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpe_16780/03_2024/8cpe_16780.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 3.05, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.93 Conformation dependent library (CDL) restraints added in 766.0 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: 0.56 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: 1.76 Time building geometry restraints manager: 4.13 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: 100.07 - 106.86: 124 106.86 - 113.65: 6300 113.65 - 120.44: 1732 120.44 - 127.23: 1729 127.23 - 134.02: 50 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 1.850 nonbonded pdb=" HG SER C 26 " pdb=" OD1 ASN B 1 " model vdw 1.493 1.850 nonbonded pdb=" OD1 ASN C 1 " pdb=" HG SER D 26 " model vdw 1.500 1.850 nonbonded pdb=" OD1 ASN D 1 " pdb=" HG SER E 26 " model vdw 1.501 1.850 nonbonded pdb=" OE1 GLN B 92 " pdb=" HH TYR B 94 " model vdw 1.526 1.850 ... (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 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 0.130 Extract box with map and model: 3.630 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 21.760 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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: 29.830 ------------------------------------------------------------------------------- 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 : 0.430 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: 0.1642 time to fit residues: 12.9742 Evaluate side-chains 25 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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: 3.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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: 0.7237 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2975 Z= 0.255 Angle : 0.605 4.565 4040 Z= 0.338 Chirality : 0.048 0.135 435 Planarity : 0.003 0.022 515 Dihedral : 7.905 23.534 400 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.75 % Favored : 93.97 % Rotamer: Outliers : 1.21 % Allowed : 10.91 % Favored : 87.88 % 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: -3.65 (0.30), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (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 0.012 0.002 PHE A 2 TYR 0.011 0.001 TYR D 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 33 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.494 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 31 average time/residue: 0.1640 time to fit residues: 7.3295 Evaluate side-chains 24 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 31 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 HIS D 35 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.4310 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= 0.255 Angle : 0.613 4.563 4040 Z= 0.341 Chirality : 0.049 0.137 435 Planarity : 0.003 0.026 515 Dihedral : 7.677 22.339 400 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 4.24 % Allowed : 14.85 % 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: -4.03 (0.29), 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 D 33 *********************** 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 41 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 27 time to evaluate : 0.460 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 37 average time/residue: 0.1650 time to fit residues: 8.5918 Evaluate side-chains 29 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 22 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 32 HIS Chi-restraints excluded: chain B residue 88 ASP 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: 3.9990 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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: 0.7424 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2975 Z= 0.292 Angle : 0.625 4.874 4040 Z= 0.346 Chirality : 0.048 0.140 435 Planarity : 0.003 0.024 515 Dihedral : 7.591 22.986 400 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 3.64 % Allowed : 16.97 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.27), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.21), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 100 HIS 0.006 0.001 HIS B 32 PHE 0.012 0.003 PHE B 102 TYR 0.011 0.001 TYR B 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 34 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 22 time to evaluate : 0.494 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 30 average time/residue: 0.1684 time to fit residues: 7.2285 Evaluate side-chains 27 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 21 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 ASP 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 Chi-restraints excluded: chain E residue 88 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 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 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.5564 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= 0.287 Angle : 0.638 5.628 4040 Z= 0.354 Chirality : 0.048 0.139 435 Planarity : 0.004 0.027 515 Dihedral : 7.589 23.767 400 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer: Outliers : 5.45 % Allowed : 15.76 % 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: -4.63 (0.26), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.20), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 100 HIS 0.003 0.001 HIS A 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 43 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 25 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7306 (tt0) REVERT: E 2 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.7267 (t80) outliers start: 18 outliers final: 11 residues processed: 40 average time/residue: 0.1967 time to fit residues: 10.4752 Evaluate side-chains 37 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 25 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 88 ASP Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 102 PHE Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 88 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 0.0980 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.5668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2975 Z= 0.128 Angle : 0.562 6.185 4040 Z= 0.306 Chirality : 0.048 0.132 435 Planarity : 0.003 0.027 515 Dihedral : 6.630 20.182 400 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.42 % Allowed : 18.48 % Favored : 79.09 % 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: -4.37 (0.27), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.21), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 36 HIS 0.007 0.001 HIS A 32 PHE 0.008 0.001 PHE A 102 TYR 0.007 0.001 TYR E 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 35 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 27 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 3 MET cc_start: 0.7570 (mtt) cc_final: 0.7031 (mtt) REVERT: A 86 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7228 (tt0) outliers start: 8 outliers final: 5 residues processed: 33 average time/residue: 0.2054 time to fit residues: 9.1241 Evaluate side-chains 27 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 22 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain A residue 32 HIS 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: 3.9990 chunk 20 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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: 0.7476 moved from start: 0.5913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2975 Z= 0.190 Angle : 0.576 5.782 4040 Z= 0.315 Chirality : 0.047 0.127 435 Planarity : 0.003 0.028 515 Dihedral : 6.712 20.510 400 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 3.64 % Allowed : 18.18 % Favored : 78.18 % 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: -4.55 (0.27), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.21), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 100 HIS 0.008 0.001 HIS A 32 PHE 0.009 0.002 PHE B 102 TYR 0.008 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 34 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 22 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 3 MET cc_start: 0.7538 (mtt) cc_final: 0.7057 (mtt) REVERT: A 86 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7236 (tt0) outliers start: 12 outliers final: 8 residues processed: 32 average time/residue: 0.2035 time to fit residues: 8.8599 Evaluate side-chains 30 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 22 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 ASP 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 B residue 88 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 0.1980 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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: 0.7444 moved from start: 0.6015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2975 Z= 0.124 Angle : 0.561 6.028 4040 Z= 0.303 Chirality : 0.047 0.124 435 Planarity : 0.003 0.027 515 Dihedral : 6.392 19.417 400 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.33 % Allowed : 18.79 % Favored : 77.88 % 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: -4.54 (0.27), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.21), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 36 HIS 0.006 0.001 HIS A 32 PHE 0.008 0.001 PHE E 102 TYR 0.008 0.001 TYR B 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 35 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 24 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 MET cc_start: 0.7505 (mtt) cc_final: 0.7004 (mtt) REVERT: A 86 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7195 (tt0) outliers start: 11 outliers final: 9 residues processed: 33 average time/residue: 0.1944 time to fit residues: 8.7485 Evaluate side-chains 31 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 22 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain B residue 32 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 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: 0.3980 chunk 29 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7440 moved from start: 0.6086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2975 Z= 0.127 Angle : 0.552 6.033 4040 Z= 0.298 Chirality : 0.047 0.124 435 Planarity : 0.003 0.027 515 Dihedral : 6.229 19.334 400 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 2.12 % Allowed : 20.30 % 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: -4.56 (0.27), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.21), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 36 HIS 0.003 0.001 HIS B 32 PHE 0.009 0.001 PHE E 102 TYR 0.009 0.001 TYR B 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 29 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 22 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 MET cc_start: 0.7529 (mtt) cc_final: 0.7006 (mtt) REVERT: A 86 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7200 (tt0) outliers start: 7 outliers final: 6 residues processed: 28 average time/residue: 0.2007 time to fit residues: 7.7895 Evaluate side-chains 27 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 21 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 91 CYS 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: 0.0060 chunk 27 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 28 optimal weight: 0.0570 chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.9518 ------------------------------------------------------------------------------- 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: 0.7471 moved from start: 0.6276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2975 Z= 0.150 Angle : 0.549 5.641 4040 Z= 0.297 Chirality : 0.047 0.127 435 Planarity : 0.003 0.026 515 Dihedral : 6.171 19.376 400 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 2.42 % Allowed : 19.70 % Favored : 77.88 % 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: -4.68 (0.27), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.21), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 36 HIS 0.006 0.001 HIS B 32 PHE 0.011 0.001 PHE E 102 TYR 0.005 0.001 TYR A 89 ********************** 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 31 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 23 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 MET cc_start: 0.7660 (mtt) cc_final: 0.7128 (mtt) REVERT: A 86 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7195 (tt0) outliers start: 8 outliers final: 8 residues processed: 30 average time/residue: 0.2067 time to fit residues: 8.6362 Evaluate side-chains 30 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 22 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 91 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.079460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.068559 restraints weight = 20717.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.071131 restraints weight = 8212.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.072815 restraints weight = 4272.088| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.6282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 2975 Z= 0.280 Angle : 1.299 57.266 4040 Z= 0.923 Chirality : 0.047 0.126 435 Planarity : 0.008 0.174 515 Dihedral : 6.146 19.374 400 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 2.12 % Allowed : 20.30 % 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: -4.69 (0.27), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.21), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 36 HIS 0.222 0.009 HIS B 32 PHE 0.009 0.001 PHE E 102 TYR 0.004 0.001 TYR A 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2293.26 seconds wall clock time: 41 minutes 0.63 seconds (2460.63 seconds total)