Starting phenix.real_space_refine on Fri Nov 15 10:08:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9faa_50270/11_2024/9faa_50270_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9faa_50270/11_2024/9faa_50270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9faa_50270/11_2024/9faa_50270.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9faa_50270/11_2024/9faa_50270.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9faa_50270/11_2024/9faa_50270_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9faa_50270/11_2024/9faa_50270_trim.cif" } resolution = 3.6 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= 0.003 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 10 5.16 5 C 2815 2.51 5 N 730 2.21 5 O 905 1.98 5 H 4235 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-5513/modules/chem_data/mon_lib" Total number of atoms: 8695 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1725 Classifications: {'peptide': 118} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 108} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, B, E, D Time building chain proxies: 4.14, per 1000 atoms: 0.48 Number of scatterers: 8695 At special positions: 0 Unit cell: (88.011, 124.46, 42.672, 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 10 16.00 O 905 8.00 N 730 7.00 C 2815 6.00 H 4235 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 87 " distance=2.02 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 Links applied NAG-ASN " NAG A 201 " - " ASN A 19 " " NAG B 201 " - " ASN B 19 " " NAG C 201 " - " ASN C 19 " " NAG D 201 " - " ASN D 19 " " NAG E 201 " - " ASN E 19 " Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 811.4 milliseconds 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1040 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 2 through 5 removed outlier: 6.194A pdb=" N GLU A 3 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.360A pdb=" N VAL D 10 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER A 9 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL B 12 " --> pdb=" O SER A 9 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER A 11 " --> pdb=" O VAL B 12 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 17 through 23 removed outlier: 6.672A pdb=" N THR A 17 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE B 20 " --> pdb=" O THR A 17 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASN A 19 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N CYS B 22 " --> pdb=" O ASN A 19 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR A 21 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 26 through 30 removed outlier: 6.588A pdb=" N TYR A 26 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N GLU B 29 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY A 28 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 36 through 37 removed outlier: 6.779A pdb=" N GLN D 36 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLN A 36 " --> pdb=" O GLN C 37 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN C 36 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 44 through 52 removed outlier: 6.662A pdb=" N VAL A 44 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ILE B 47 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A 46 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLN B 49 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR A 48 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N SER B 51 " --> pdb=" O TYR A 48 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N SER A 50 " --> pdb=" O SER B 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 64 through 65 removed outlier: 6.621A pdb=" N SER A 62 " --> pdb=" O GLY B 63 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ASN B 65 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER A 64 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 72 through 75 removed outlier: 6.788A pdb=" N LEU D 72 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N SER B 75 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE D 74 " --> pdb=" O SER B 75 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR A 73 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU A 72 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N SER C 75 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A 74 " --> pdb=" O SER C 75 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU C 72 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N SER E 75 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE C 74 " --> pdb=" O SER E 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 84 through 86 removed outlier: 6.542A pdb=" N ALA A 83 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N PHE B 86 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR A 85 " --> pdb=" O PHE B 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 89 through 97 removed outlier: 6.457A pdb=" N TRP D 90 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N THR B 93 " --> pdb=" O TRP D 90 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE D 92 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL B 95 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N SER D 94 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N PHE B 97 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL D 96 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N PHE A 97 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TRP A 90 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N THR C 93 " --> pdb=" O TRP A 90 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N PHE A 92 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL C 95 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER A 94 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE C 97 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL A 96 " --> pdb=" O PHE C 97 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TRP C 90 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N THR E 93 " --> pdb=" O TRP C 90 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N PHE C 92 " --> pdb=" O THR E 93 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL E 95 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER C 94 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N PHE E 97 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL C 96 " --> pdb=" O PHE E 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 102 through 106 removed outlier: 6.707A pdb=" N LEU D 103 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU B 106 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL D 105 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU A 103 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU C 106 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL A 105 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU C 103 " --> pdb=" O THR E 104 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU E 106 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL C 105 " --> pdb=" O LEU E 106 " (cutoff:3.500A) 93 hydrogen bonds defined for protein. 270 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.87 Time building geometry restraints manager: 2.60 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: 4235 1.03 - 1.22: 5 1.22 - 1.42: 1960 1.42 - 1.61: 2600 1.61 - 1.81: 10 Bond restraints: 8810 Sorted by residual: bond pdb=" CB ILE E 20 " pdb=" CG2 ILE E 20 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.41e+00 bond pdb=" CB ILE B 20 " pdb=" CG2 ILE B 20 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.34e+00 bond pdb=" CA GLY C 67 " pdb=" C GLY C 67 " ideal model delta sigma weight residual 1.516 1.498 0.018 1.18e-02 7.18e+03 2.34e+00 bond pdb=" CB ILE C 20 " pdb=" CG2 ILE C 20 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.33e+00 bond pdb=" CB ILE A 20 " pdb=" CG2 ILE A 20 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.29e+00 ... (remaining 8805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 14447 1.41 - 2.82: 1160 2.82 - 4.23: 173 4.23 - 5.64: 40 5.64 - 7.05: 10 Bond angle restraints: 15830 Sorted by residual: angle pdb=" N THR A 69 " pdb=" CA THR A 69 " pdb=" C THR A 69 " ideal model delta sigma weight residual 109.94 102.89 7.05 1.57e+00 4.06e-01 2.02e+01 angle pdb=" N THR D 69 " pdb=" CA THR D 69 " pdb=" C THR D 69 " ideal model delta sigma weight residual 109.94 102.91 7.03 1.57e+00 4.06e-01 2.00e+01 angle pdb=" N THR E 69 " pdb=" CA THR E 69 " pdb=" C THR E 69 " ideal model delta sigma weight residual 109.94 102.93 7.01 1.57e+00 4.06e-01 1.99e+01 angle pdb=" N THR B 69 " pdb=" CA THR B 69 " pdb=" C THR B 69 " ideal model delta sigma weight residual 109.94 102.93 7.01 1.57e+00 4.06e-01 1.99e+01 angle pdb=" N THR C 69 " pdb=" CA THR C 69 " pdb=" C THR C 69 " ideal model delta sigma weight residual 109.94 102.95 6.99 1.57e+00 4.06e-01 1.98e+01 ... (remaining 15825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.86: 3764 14.86 - 29.73: 338 29.73 - 44.59: 111 44.59 - 59.45: 95 59.45 - 74.31: 30 Dihedral angle restraints: 4338 sinusoidal: 2378 harmonic: 1960 Sorted by residual: dihedral pdb=" CA PHE B 61 " pdb=" C PHE B 61 " pdb=" N SER B 62 " pdb=" CA SER B 62 " ideal model delta harmonic sigma weight residual 180.00 164.55 15.45 0 5.00e+00 4.00e-02 9.55e+00 dihedral pdb=" CA PHE D 61 " pdb=" C PHE D 61 " pdb=" N SER D 62 " pdb=" CA SER D 62 " ideal model delta harmonic sigma weight residual 180.00 164.55 15.45 0 5.00e+00 4.00e-02 9.54e+00 dihedral pdb=" CA PHE E 61 " pdb=" C PHE E 61 " pdb=" N SER E 62 " pdb=" CA SER E 62 " ideal model delta harmonic sigma weight residual 180.00 164.56 15.44 0 5.00e+00 4.00e-02 9.54e+00 ... (remaining 4335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 476 0.048 - 0.096: 181 0.096 - 0.144: 43 0.144 - 0.192: 0 0.192 - 0.241: 5 Chirality restraints: 705 Sorted by residual: chirality pdb=" C1 NAG A 201 " pdb=" ND2 ASN A 19 " pdb=" C2 NAG A 201 " pdb=" O5 NAG A 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C1 NAG E 201 " pdb=" ND2 ASN E 19 " pdb=" C2 NAG E 201 " pdb=" O5 NAG E 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C1 NAG D 201 " pdb=" ND2 ASN D 19 " pdb=" C2 NAG D 201 " pdb=" O5 NAG D 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 702 not shown) Planarity restraints: 1350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN E 49 " 0.029 2.00e-02 2.50e+03 3.69e-02 2.04e+01 pdb=" CD GLN E 49 " -0.022 2.00e-02 2.50e+03 pdb=" OE1 GLN E 49 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 GLN E 49 " -0.060 2.00e-02 2.50e+03 pdb="HE21 GLN E 49 " -0.001 2.00e-02 2.50e+03 pdb="HE22 GLN E 49 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 49 " 0.029 2.00e-02 2.50e+03 3.68e-02 2.03e+01 pdb=" CD GLN D 49 " -0.022 2.00e-02 2.50e+03 pdb=" OE1 GLN D 49 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 GLN D 49 " -0.060 2.00e-02 2.50e+03 pdb="HE21 GLN D 49 " -0.001 2.00e-02 2.50e+03 pdb="HE22 GLN D 49 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 49 " 0.029 2.00e-02 2.50e+03 3.68e-02 2.03e+01 pdb=" CD GLN A 49 " -0.022 2.00e-02 2.50e+03 pdb=" OE1 GLN A 49 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 GLN A 49 " -0.060 2.00e-02 2.50e+03 pdb="HE21 GLN A 49 " -0.001 2.00e-02 2.50e+03 pdb="HE22 GLN A 49 " 0.056 2.00e-02 2.50e+03 ... (remaining 1347 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 187 2.09 - 2.72: 14912 2.72 - 3.34: 22425 3.34 - 3.97: 31298 3.97 - 4.60: 46361 Nonbonded interactions: 115183 Sorted by model distance: nonbonded pdb=" H ASN A 68 " pdb=" OD1 ASN B 68 " model vdw 1.461 2.450 nonbonded pdb=" OD1 ASN A 68 " pdb=" H ASN C 68 " model vdw 1.553 2.450 nonbonded pdb=" OD1 ASN C 68 " pdb=" H ASN E 68 " model vdw 1.598 2.450 nonbonded pdb=" OD1 ASN D 68 " pdb=" H ASN B 68 " model vdw 1.649 2.450 nonbonded pdb="HG21 THR E 69 " pdb=" H ALA E 70 " model vdw 1.788 2.270 ... (remaining 115178 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.150 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.750 Find NCS groups from input model: 0.250 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 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 : 0.010 0.053 4575 Z= 0.675 Angle : 1.099 7.048 6240 Z= 0.623 Chirality : 0.053 0.241 705 Planarity : 0.006 0.042 805 Dihedral : 11.734 74.313 1690 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.24), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.19), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.008 TRP E 90 PHE 0.021 0.005 PHE C 61 TYR 0.038 0.007 TYR B 85 ARG 0.009 0.003 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8275 (t) cc_final: 0.7998 (m) REVERT: A 91 ASP cc_start: 0.7857 (t0) cc_final: 0.7645 (t0) REVERT: A 108 GLN cc_start: 0.7845 (pt0) cc_final: 0.7535 (pp30) REVERT: A 117 LEU cc_start: 0.5983 (mt) cc_final: 0.5694 (mt) REVERT: D 49 GLN cc_start: 0.7584 (tt0) cc_final: 0.7383 (tt0) REVERT: D 108 GLN cc_start: 0.7793 (pt0) cc_final: 0.7496 (pp30) REVERT: C 108 GLN cc_start: 0.7868 (pt0) cc_final: 0.7408 (pp30) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.2706 time to fit residues: 27.3344 Evaluate side-chains 48 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 16 optimal weight: 0.0070 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 4575 Z= 0.184 Angle : 0.616 4.358 6240 Z= 0.324 Chirality : 0.051 0.252 705 Planarity : 0.005 0.045 805 Dihedral : 6.183 23.544 730 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.22 % Allowed : 4.69 % Favored : 94.08 % 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: -3.85 (0.25), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.19), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 34 PHE 0.013 0.001 PHE D 2 TYR 0.014 0.002 TYR C 85 ARG 0.003 0.000 ARG E 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8184 (t) cc_final: 0.7900 (m) REVERT: A 31 TYR cc_start: 0.8069 (m-80) cc_final: 0.7849 (m-80) REVERT: A 108 GLN cc_start: 0.7807 (pt0) cc_final: 0.7601 (pp30) REVERT: A 117 LEU cc_start: 0.5988 (mt) cc_final: 0.5765 (mt) REVERT: D 108 GLN cc_start: 0.7776 (pt0) cc_final: 0.7412 (pp30) REVERT: C 91 ASP cc_start: 0.7795 (t0) cc_final: 0.7409 (m-30) REVERT: C 108 GLN cc_start: 0.7912 (pt0) cc_final: 0.7420 (pp30) REVERT: E 91 ASP cc_start: 0.8007 (t0) cc_final: 0.7453 (m-30) outliers start: 6 outliers final: 2 residues processed: 64 average time/residue: 0.2808 time to fit residues: 24.3807 Evaluate side-chains 53 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain B residue 17 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 40 optimal weight: 0.1980 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 4575 Z= 0.370 Angle : 0.694 7.116 6240 Z= 0.362 Chirality : 0.049 0.196 705 Planarity : 0.005 0.042 805 Dihedral : 6.849 34.344 730 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.63 % Allowed : 6.94 % Favored : 91.43 % 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: -3.86 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 34 PHE 0.015 0.002 PHE B 61 TYR 0.020 0.002 TYR D 85 ARG 0.002 0.000 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8205 (t) cc_final: 0.7907 (m) REVERT: A 31 TYR cc_start: 0.8195 (m-80) cc_final: 0.7974 (m-80) REVERT: A 108 GLN cc_start: 0.7909 (pt0) cc_final: 0.7567 (pp30) REVERT: D 108 GLN cc_start: 0.7917 (pt0) cc_final: 0.7529 (pp30) REVERT: C 108 GLN cc_start: 0.8061 (pt0) cc_final: 0.7305 (pp30) REVERT: E 91 ASP cc_start: 0.8074 (t0) cc_final: 0.7414 (m-30) outliers start: 8 outliers final: 7 residues processed: 60 average time/residue: 0.2767 time to fit residues: 22.3284 Evaluate side-chains 55 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4575 Z= 0.189 Angle : 0.568 4.328 6240 Z= 0.296 Chirality : 0.049 0.229 705 Planarity : 0.005 0.041 805 Dihedral : 6.183 28.964 730 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.04 % Allowed : 6.94 % Favored : 91.02 % 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: -3.96 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 34 PHE 0.009 0.001 PHE A 61 TYR 0.011 0.001 TYR A 85 ARG 0.002 0.000 ARG E 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8245 (t) cc_final: 0.7909 (m) REVERT: A 108 GLN cc_start: 0.7913 (pt0) cc_final: 0.7058 (pp30) REVERT: D 108 GLN cc_start: 0.7934 (pt0) cc_final: 0.7505 (pp30) REVERT: C 108 GLN cc_start: 0.8038 (pt0) cc_final: 0.7288 (pp30) REVERT: E 91 ASP cc_start: 0.8045 (t0) cc_final: 0.7413 (m-30) outliers start: 10 outliers final: 9 residues processed: 66 average time/residue: 0.2752 time to fit residues: 24.5088 Evaluate side-chains 61 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain E residue 68 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4575 Z= 0.188 Angle : 0.552 4.132 6240 Z= 0.285 Chirality : 0.048 0.214 705 Planarity : 0.005 0.043 805 Dihedral : 6.060 29.660 730 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.63 % Allowed : 8.16 % Favored : 90.20 % 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: -3.95 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 34 PHE 0.009 0.001 PHE B 61 TYR 0.009 0.001 TYR C 85 ARG 0.001 0.000 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8264 (t) cc_final: 0.7904 (m) REVERT: A 108 GLN cc_start: 0.7885 (pt0) cc_final: 0.7036 (pp30) REVERT: D 69 THR cc_start: 0.7205 (m) cc_final: 0.6680 (p) REVERT: D 108 GLN cc_start: 0.7988 (pt0) cc_final: 0.7502 (pp30) REVERT: C 108 GLN cc_start: 0.8005 (pt0) cc_final: 0.7268 (pp30) REVERT: E 91 ASP cc_start: 0.8067 (t0) cc_final: 0.7413 (m-30) outliers start: 8 outliers final: 7 residues processed: 65 average time/residue: 0.2783 time to fit residues: 24.2724 Evaluate side-chains 57 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain E residue 68 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 4575 Z= 0.326 Angle : 0.644 5.033 6240 Z= 0.337 Chirality : 0.048 0.197 705 Planarity : 0.005 0.044 805 Dihedral : 6.930 38.196 730 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.24 % Allowed : 8.78 % Favored : 88.98 % 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: -3.99 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 34 PHE 0.013 0.002 PHE A 61 TYR 0.017 0.002 TYR C 85 ARG 0.002 0.000 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8306 (t) cc_final: 0.7942 (m) REVERT: D 108 GLN cc_start: 0.8117 (pt0) cc_final: 0.7569 (pp30) outliers start: 11 outliers final: 9 residues processed: 60 average time/residue: 0.2765 time to fit residues: 22.5750 Evaluate side-chains 56 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain E residue 68 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4575 Z= 0.174 Angle : 0.557 3.897 6240 Z= 0.289 Chirality : 0.048 0.223 705 Planarity : 0.005 0.048 805 Dihedral : 6.145 30.660 730 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.22 % Allowed : 10.82 % Favored : 87.96 % 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: -4.00 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 34 PHE 0.009 0.001 PHE B 61 TYR 0.009 0.001 TYR A 85 ARG 0.002 0.000 ARG E 60 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8318 (t) cc_final: 0.7936 (m) REVERT: D 8 SER cc_start: 0.8237 (OUTLIER) cc_final: 0.7911 (p) REVERT: D 108 GLN cc_start: 0.8099 (pt0) cc_final: 0.7555 (pp30) outliers start: 6 outliers final: 5 residues processed: 59 average time/residue: 0.2879 time to fit residues: 22.7226 Evaluate side-chains 54 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 101 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 49 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4575 Z= 0.164 Angle : 0.543 4.553 6240 Z= 0.281 Chirality : 0.048 0.208 705 Planarity : 0.005 0.046 805 Dihedral : 5.932 28.787 730 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.63 % Allowed : 10.41 % Favored : 87.96 % 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: -3.99 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 90 PHE 0.009 0.001 PHE D 61 TYR 0.007 0.001 TYR C 85 ARG 0.001 0.000 ARG E 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8323 (t) cc_final: 0.7931 (m) REVERT: D 8 SER cc_start: 0.8231 (OUTLIER) cc_final: 0.7895 (p) REVERT: D 108 GLN cc_start: 0.8085 (pt0) cc_final: 0.7551 (pp30) outliers start: 8 outliers final: 6 residues processed: 57 average time/residue: 0.2842 time to fit residues: 21.7634 Evaluate side-chains 55 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 101 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4575 Z= 0.182 Angle : 0.543 3.915 6240 Z= 0.280 Chirality : 0.047 0.197 705 Planarity : 0.005 0.047 805 Dihedral : 5.922 30.467 730 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.63 % Allowed : 10.00 % Favored : 88.37 % 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: -3.96 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 34 PHE 0.010 0.001 PHE A 61 TYR 0.009 0.001 TYR C 85 ARG 0.001 0.000 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 8 SER cc_start: 0.8247 (OUTLIER) cc_final: 0.7924 (p) REVERT: D 108 GLN cc_start: 0.8093 (pt0) cc_final: 0.7545 (pp30) outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 0.2776 time to fit residues: 22.1454 Evaluate side-chains 54 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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: 0.7592 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4575 Z= 0.205 Angle : 0.554 4.621 6240 Z= 0.286 Chirality : 0.047 0.196 705 Planarity : 0.005 0.047 805 Dihedral : 6.061 32.330 730 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.43 % Allowed : 10.20 % Favored : 88.37 % 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: -4.00 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 34 PHE 0.010 0.001 PHE A 61 TYR 0.009 0.001 TYR C 85 ARG 0.001 0.000 ARG E 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8359 (t) cc_final: 0.7952 (m) REVERT: D 8 SER cc_start: 0.8253 (OUTLIER) cc_final: 0.7903 (p) REVERT: D 108 GLN cc_start: 0.8111 (pt0) cc_final: 0.7551 (pp30) outliers start: 7 outliers final: 6 residues processed: 54 average time/residue: 0.2886 time to fit residues: 20.9593 Evaluate side-chains 53 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.4354 r_free = 0.4354 target = 0.119513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.102585 restraints weight = 27579.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.105925 restraints weight = 10599.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.108007 restraints weight = 5508.778| |-----------------------------------------------------------------------------| r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4575 Z= 0.209 Angle : 0.554 4.376 6240 Z= 0.287 Chirality : 0.047 0.199 705 Planarity : 0.005 0.048 805 Dihedral : 6.138 33.515 730 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.63 % Allowed : 10.20 % Favored : 88.16 % 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: -4.00 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 34 PHE 0.010 0.001 PHE A 61 TYR 0.009 0.001 TYR C 85 ARG 0.002 0.000 ARG A 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2713.04 seconds wall clock time: 49 minutes 1.34 seconds (2941.34 seconds total)