Starting phenix.real_space_refine on Wed Mar 5 17:00:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8az2_15730/03_2025/8az2_15730.cif Found real_map, /net/cci-nas-00/data/ceres_data/8az2_15730/03_2025/8az2_15730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8az2_15730/03_2025/8az2_15730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8az2_15730/03_2025/8az2_15730.map" model { file = "/net/cci-nas-00/data/ceres_data/8az2_15730/03_2025/8az2_15730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8az2_15730/03_2025/8az2_15730.cif" } resolution = 3.4 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= 0.004 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: 3 Type Number sf(0) Gaussians C 1815 2.51 5 N 545 2.21 5 O 575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2935 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 182 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 182 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 182 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 182 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 182 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.58, per 1000 atoms: 0.88 Number of scatterers: 2935 At special positions: 0 Unit cell: (67.2, 93.24, 39.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 575 8.00 N 545 7.00 C 1815 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=15, symmetry=0 Number of additional bonds: simple=15, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 384.4 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 13 sheets defined 0.0% alpha, 45.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 23 removed outlier: 6.561A pdb=" N ASN A 22 " --> pdb=" O PHE D 23 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN D 22 " --> pdb=" O PHE G 23 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASN G 22 " --> pdb=" O PHE J 23 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASN J 22 " --> pdb=" O PHE M 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 32 removed outlier: 8.486A pdb=" N THR A 30 " --> pdb=" O ASN D 31 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N THR D 30 " --> pdb=" O ASN G 31 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N THR G 30 " --> pdb=" O ASN J 31 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N THR J 30 " --> pdb=" O ASN M 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA6, first strand: chain 'B' and resid 14 through 19 Processing sheet with id=AA7, first strand: chain 'B' and resid 22 through 23 removed outlier: 6.424A pdb=" N ASN B 22 " --> pdb=" O PHE E 23 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN E 22 " --> pdb=" O PHE H 23 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN H 22 " --> pdb=" O PHE K 23 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASN K 22 " --> pdb=" O PHE N 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AA9, first strand: chain 'B' and resid 30 through 32 removed outlier: 8.462A pdb=" N THR B 30 " --> pdb=" O ASN E 31 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N THR E 30 " --> pdb=" O ASN H 31 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N THR H 30 " --> pdb=" O ASN K 31 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N THR K 30 " --> pdb=" O ASN N 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 35 through 36 removed outlier: 6.032A pdb=" N ASN E 35 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ASN H 35 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ASN K 35 " --> pdb=" O THR H 36 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASN N 35 " --> pdb=" O THR K 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 12 through 18 removed outlier: 6.369A pdb=" N LEU C 12 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N PHE F 15 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASN C 14 " --> pdb=" O PHE F 15 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL F 17 " --> pdb=" O ASN C 14 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU C 16 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU F 12 " --> pdb=" O ALA I 13 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N PHE I 15 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASN F 14 " --> pdb=" O PHE I 15 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL I 17 " --> pdb=" O ASN F 14 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU F 16 " --> pdb=" O VAL I 17 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU I 12 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N PHE L 15 " --> pdb=" O LEU I 12 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ASN I 14 " --> pdb=" O PHE L 15 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL L 17 " --> pdb=" O ASN I 14 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU I 16 " --> pdb=" O VAL L 17 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU L 12 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N PHE O 15 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN L 14 " --> pdb=" O PHE O 15 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL O 17 " --> pdb=" O ASN L 14 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU L 16 " --> pdb=" O VAL O 17 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 25 through 32 Processing sheet with id=AB4, first strand: chain 'C' and resid 35 through 36 removed outlier: 6.304A pdb=" N ASN C 35 " --> pdb=" O THR F 36 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN F 35 " --> pdb=" O THR I 36 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASN I 35 " --> pdb=" O THR L 36 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASN L 35 " --> pdb=" O THR O 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 88 hydrogen bonds defined for protein. 264 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: 0.78 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 470 1.29 - 1.35: 526 1.35 - 1.42: 361 1.42 - 1.48: 453 1.48 - 1.54: 1155 Bond restraints: 2965 Sorted by residual: bond pdb=" N GLY O 33 " pdb=" CA GLY O 33 " ideal model delta sigma weight residual 1.449 1.461 -0.012 1.45e-02 4.76e+03 7.09e-01 bond pdb=" N GLY F 33 " pdb=" CA GLY F 33 " ideal model delta sigma weight residual 1.449 1.461 -0.012 1.45e-02 4.76e+03 6.71e-01 bond pdb=" N GLY C 33 " pdb=" CA GLY C 33 " ideal model delta sigma weight residual 1.449 1.461 -0.012 1.45e-02 4.76e+03 6.30e-01 bond pdb=" N GLY L 33 " pdb=" CA GLY L 33 " ideal model delta sigma weight residual 1.449 1.461 -0.012 1.45e-02 4.76e+03 6.29e-01 bond pdb=" N GLY I 33 " pdb=" CA GLY I 33 " ideal model delta sigma weight residual 1.449 1.459 -0.010 1.45e-02 4.76e+03 4.99e-01 ... (remaining 2960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.62: 3513 0.62 - 1.23: 381 1.23 - 1.85: 88 1.85 - 2.47: 23 2.47 - 3.08: 10 Bond angle restraints: 4015 Sorted by residual: angle pdb=" NE ARG J 11 " pdb=" CZ ARG J 11 " pdb=" NH1 ARG J 11 " ideal model delta sigma weight residual 121.50 120.05 1.45 1.00e+00 1.00e+00 2.11e+00 angle pdb=" NE ARG G 11 " pdb=" CZ ARG G 11 " pdb=" NH1 ARG G 11 " ideal model delta sigma weight residual 121.50 120.07 1.43 1.00e+00 1.00e+00 2.05e+00 angle pdb=" N GLY N 20 " pdb=" CA GLY N 20 " pdb=" C GLY N 20 " ideal model delta sigma weight residual 113.48 115.56 -2.08 1.46e+00 4.69e-01 2.02e+00 angle pdb=" NE ARG F 11 " pdb=" CZ ARG F 11 " pdb=" NH1 ARG F 11 " ideal model delta sigma weight residual 121.50 120.10 1.40 1.00e+00 1.00e+00 1.97e+00 angle pdb=" N GLY E 20 " pdb=" CA GLY E 20 " pdb=" C GLY E 20 " ideal model delta sigma weight residual 113.48 115.53 -2.05 1.46e+00 4.69e-01 1.97e+00 ... (remaining 4010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.63: 1370 7.63 - 15.26: 200 15.26 - 22.90: 52 22.90 - 30.53: 8 30.53 - 38.16: 15 Dihedral angle restraints: 1645 sinusoidal: 550 harmonic: 1095 Sorted by residual: dihedral pdb=" CA SER K 19 " pdb=" C SER K 19 " pdb=" N GLY K 20 " pdb=" CA GLY K 20 " ideal model delta harmonic sigma weight residual 180.00 166.72 13.28 0 5.00e+00 4.00e-02 7.05e+00 dihedral pdb=" CA SER B 19 " pdb=" C SER B 19 " pdb=" N GLY B 20 " pdb=" CA GLY B 20 " ideal model delta harmonic sigma weight residual 180.00 166.76 13.24 0 5.00e+00 4.00e-02 7.01e+00 dihedral pdb=" CA SER E 19 " pdb=" C SER E 19 " pdb=" N GLY E 20 " pdb=" CA GLY E 20 " ideal model delta harmonic sigma weight residual 180.00 166.88 13.12 0 5.00e+00 4.00e-02 6.88e+00 ... (remaining 1642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 257 0.026 - 0.051: 124 0.051 - 0.077: 38 0.077 - 0.102: 31 0.102 - 0.128: 15 Chirality restraints: 465 Sorted by residual: chirality pdb=" CA ILE K 26 " pdb=" N ILE K 26 " pdb=" C ILE K 26 " pdb=" CB ILE K 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE F 26 " pdb=" N ILE F 26 " pdb=" C ILE F 26 " pdb=" CB ILE F 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA ILE I 26 " pdb=" N ILE I 26 " pdb=" C ILE I 26 " pdb=" CB ILE I 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 462 not shown) Planarity restraints: 525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 28 " 0.002 2.00e-02 2.50e+03 3.97e-03 1.58e-01 pdb=" C SER B 28 " -0.007 2.00e-02 2.50e+03 pdb=" O SER B 28 " 0.003 2.00e-02 2.50e+03 pdb=" N SER B 29 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER K 28 " 0.002 2.00e-02 2.50e+03 3.74e-03 1.40e-01 pdb=" C SER K 28 " -0.006 2.00e-02 2.50e+03 pdb=" O SER K 28 " 0.002 2.00e-02 2.50e+03 pdb=" N SER K 29 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY K 20 " -0.002 2.00e-02 2.50e+03 3.66e-03 1.34e-01 pdb=" C GLY K 20 " 0.006 2.00e-02 2.50e+03 pdb=" O GLY K 20 " -0.002 2.00e-02 2.50e+03 pdb=" N ASN K 21 " -0.002 2.00e-02 2.50e+03 ... (remaining 522 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 1227 2.91 - 3.41: 2380 3.41 - 3.90: 5126 3.90 - 4.40: 5743 4.40 - 4.90: 10542 Nonbonded interactions: 25018 Sorted by model distance: nonbonded pdb=" O SER E 19 " pdb=" ND2 ASN E 21 " model vdw 2.412 3.120 nonbonded pdb=" O SER N 19 " pdb=" ND2 ASN N 21 " model vdw 2.412 3.120 nonbonded pdb=" O SER K 19 " pdb=" ND2 ASN K 21 " model vdw 2.424 3.120 nonbonded pdb=" O SER B 19 " pdb=" ND2 ASN B 21 " model vdw 2.424 3.120 nonbonded pdb=" O SER H 19 " pdb=" ND2 ASN H 21 " model vdw 2.447 3.120 ... (remaining 25013 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' and (resid 13 through 37 or resid 38)) selection = chain 'B' selection = (chain 'C' and (resid 13 through 37 or resid 38)) selection = (chain 'D' and (resid 13 through 37 or resid 38)) selection = chain 'E' selection = (chain 'F' and (resid 13 through 37 or resid 38)) selection = (chain 'G' and (resid 13 through 37 or resid 38)) selection = chain 'H' selection = (chain 'I' and (resid 13 through 37 or resid 38)) selection = (chain 'J' and (resid 13 through 37 or resid 38)) selection = chain 'K' selection = (chain 'L' and (resid 13 through 37 or resid 38)) selection = (chain 'M' and (resid 13 through 37 or resid 38)) selection = chain 'N' selection = (chain 'O' and (resid 13 through 37 or resid 38)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.980 Find NCS groups from input model: 0.180 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 : 0.003 0.016 2965 Z= 0.199 Angle : 0.453 3.082 4015 Z= 0.262 Chirality : 0.042 0.128 465 Planarity : 0.001 0.004 525 Dihedral : 9.018 38.160 945 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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: -2.98 (0.27), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.21), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 18 PHE 0.003 0.001 PHE H 15 TYR 0.003 0.001 TYR A 37 ARG 0.001 0.000 ARG C 11 *********************** 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 18 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.292 Fit side-chains REVERT: C 37 TYR cc_start: 0.8715 (m-80) cc_final: 0.8501 (m-80) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0927 time to fit residues: 2.6357 Evaluate side-chains 14 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN B 14 ASN B 35 ASN C 35 ASN D 35 ASN E 35 ASN F 35 ASN G 18 HIS G 35 ASN H 14 ASN H 35 ASN I 35 ASN J 22 ASN J 35 ASN K 14 ASN K 35 ASN L 35 ASN M 22 ASN M 35 ASN N 14 ASN N 21 ASN N 35 ASN O 35 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.117853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.076811 restraints weight = 2946.195| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.72 r_work: 0.3055 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 2965 Z= 0.340 Angle : 0.502 3.390 4015 Z= 0.282 Chirality : 0.046 0.134 465 Planarity : 0.002 0.012 525 Dihedral : 5.010 19.931 405 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.25 % Allowed : 1.88 % Favored : 96.88 % 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: -2.91 (0.29), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.22), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS J 18 PHE 0.010 0.002 PHE L 23 TYR 0.011 0.001 TYR D 37 ARG 0.002 0.000 ARG G 11 *********************** 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 15 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 11 time to evaluate : 0.291 Fit side-chains REVERT: D 31 ASN cc_start: 0.8231 (t0) cc_final: 0.7987 (t0) outliers start: 4 outliers final: 4 residues processed: 15 average time/residue: 0.0761 time to fit residues: 1.9920 Evaluate side-chains 15 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 11 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain M residue 28 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.119720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.078346 restraints weight = 2896.068| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.73 r_work: 0.3080 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2965 Z= 0.224 Angle : 0.440 3.246 4015 Z= 0.248 Chirality : 0.045 0.132 465 Planarity : 0.002 0.012 525 Dihedral : 4.561 19.029 405 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.25 % Allowed : 3.44 % Favored : 95.31 % 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: -2.91 (0.29), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.22), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS J 18 PHE 0.008 0.001 PHE L 23 TYR 0.008 0.001 TYR D 37 ARG 0.000 0.000 ARG G 11 *********************** 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 14 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 10 time to evaluate : 0.287 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 14 average time/residue: 0.0812 time to fit residues: 1.9449 Evaluate side-chains 14 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 10 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain M residue 28 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.117066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.076146 restraints weight = 3098.252| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.72 r_work: 0.3036 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 2965 Z= 0.326 Angle : 0.465 3.482 4015 Z= 0.265 Chirality : 0.045 0.133 465 Planarity : 0.002 0.013 525 Dihedral : 4.861 19.835 405 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.25 % Allowed : 5.94 % Favored : 92.81 % 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: -2.97 (0.30), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS J 18 PHE 0.010 0.001 PHE I 23 TYR 0.009 0.001 TYR D 37 ARG 0.001 0.000 ARG O 11 *********************** 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 16 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 12 time to evaluate : 0.303 Fit side-chains REVERT: O 23 PHE cc_start: 0.8063 (m-80) cc_final: 0.7800 (m-80) outliers start: 4 outliers final: 4 residues processed: 16 average time/residue: 0.0859 time to fit residues: 2.2894 Evaluate side-chains 16 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 12 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain M residue 28 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 24 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.122797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.081306 restraints weight = 3103.164| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.77 r_work: 0.3129 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 2965 Z= 0.107 Angle : 0.401 3.437 4015 Z= 0.224 Chirality : 0.044 0.129 465 Planarity : 0.001 0.005 525 Dihedral : 4.075 16.757 405 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.25 % Allowed : 6.56 % Favored : 92.19 % 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: -2.90 (0.30), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS M 18 PHE 0.007 0.001 PHE L 23 TYR 0.007 0.001 TYR B 37 ARG 0.000 0.000 ARG D 11 *********************** 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 17 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 13 time to evaluate : 0.321 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 17 average time/residue: 0.0860 time to fit residues: 2.4048 Evaluate side-chains 15 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 11 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain M residue 28 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN D 18 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.112223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.071431 restraints weight = 3223.258| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.71 r_work: 0.2973 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.044 2965 Z= 0.652 Angle : 0.597 3.806 4015 Z= 0.347 Chirality : 0.050 0.184 465 Planarity : 0.004 0.021 525 Dihedral : 5.772 23.645 405 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.25 % Allowed : 7.50 % Favored : 91.25 % 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: -3.16 (0.30), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS J 18 PHE 0.014 0.003 PHE J 15 TYR 0.012 0.002 TYR J 37 ARG 0.002 0.001 ARG O 11 *********************** 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 22 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.269 Fit side-chains REVERT: C 35 ASN cc_start: 0.8622 (m-40) cc_final: 0.8392 (m110) outliers start: 4 outliers final: 4 residues processed: 22 average time/residue: 0.0760 time to fit residues: 2.6425 Evaluate side-chains 22 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain M residue 28 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 21 ASN F 35 ASN H 21 ASN K 21 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.118345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.076806 restraints weight = 3207.178| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.85 r_work: 0.3051 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2965 Z= 0.182 Angle : 0.449 4.139 4015 Z= 0.252 Chirality : 0.045 0.136 465 Planarity : 0.001 0.006 525 Dihedral : 4.792 18.725 405 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.25 % Allowed : 7.81 % Favored : 90.94 % 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: -3.18 (0.30), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 18 PHE 0.011 0.001 PHE I 23 TYR 0.007 0.001 TYR D 37 ARG 0.000 0.000 ARG A 11 *********************** 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 17 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 13 time to evaluate : 0.322 Fit side-chains REVERT: C 35 ASN cc_start: 0.8453 (m-40) cc_final: 0.8253 (m110) REVERT: O 23 PHE cc_start: 0.7958 (m-80) cc_final: 0.7732 (m-80) REVERT: O 37 TYR cc_start: 0.9014 (m-80) cc_final: 0.8593 (m-80) outliers start: 4 outliers final: 4 residues processed: 17 average time/residue: 0.0835 time to fit residues: 2.3824 Evaluate side-chains 17 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 13 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain M residue 28 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.114386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.073229 restraints weight = 3173.951| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.74 r_work: 0.3002 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 2965 Z= 0.442 Angle : 0.520 4.014 4015 Z= 0.300 Chirality : 0.047 0.137 465 Planarity : 0.003 0.014 525 Dihedral : 5.390 21.765 405 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 1.25 % Allowed : 8.44 % Favored : 90.31 % 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: -3.13 (0.30), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS J 18 PHE 0.011 0.002 PHE C 23 TYR 0.008 0.001 TYR J 37 ARG 0.001 0.000 ARG C 11 *********************** 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 20 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.318 Fit side-chains REVERT: C 35 ASN cc_start: 0.8504 (m-40) cc_final: 0.8268 (m110) outliers start: 4 outliers final: 4 residues processed: 20 average time/residue: 0.0812 time to fit residues: 2.6415 Evaluate side-chains 20 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain M residue 28 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.3581 r_free = 0.3581 target = 0.117483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.076108 restraints weight = 3097.908| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.73 r_work: 0.3047 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2965 Z= 0.282 Angle : 0.470 4.157 4015 Z= 0.268 Chirality : 0.046 0.138 465 Planarity : 0.002 0.009 525 Dihedral : 5.017 19.502 405 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.25 % Allowed : 8.12 % Favored : 90.62 % 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: -3.09 (0.30), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS J 18 PHE 0.012 0.001 PHE I 23 TYR 0.007 0.001 TYR D 37 ARG 0.001 0.000 ARG C 11 *********************** 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 20 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.330 Fit side-chains REVERT: C 35 ASN cc_start: 0.8528 (m-40) cc_final: 0.8290 (m110) REVERT: O 23 PHE cc_start: 0.8085 (m-80) cc_final: 0.7868 (m-80) outliers start: 4 outliers final: 4 residues processed: 20 average time/residue: 0.0812 time to fit residues: 2.6467 Evaluate side-chains 20 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain M residue 28 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 29 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.113314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.072773 restraints weight = 3357.054| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.80 r_work: 0.2983 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.039 2965 Z= 0.527 Angle : 0.559 4.144 4015 Z= 0.325 Chirality : 0.048 0.138 465 Planarity : 0.003 0.017 525 Dihedral : 5.729 22.088 405 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 1.25 % Allowed : 8.75 % Favored : 90.00 % 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: -3.10 (0.30), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS J 18 PHE 0.012 0.002 PHE C 23 TYR 0.009 0.002 TYR J 37 ARG 0.001 0.000 ARG L 11 ********************** 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 25 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.291 Fit side-chains REVERT: C 35 ASN cc_start: 0.8584 (m-40) cc_final: 0.8322 (m110) REVERT: D 31 ASN cc_start: 0.8273 (t0) cc_final: 0.7975 (t0) outliers start: 4 outliers final: 4 residues processed: 25 average time/residue: 0.0749 time to fit residues: 2.9519 Evaluate side-chains 25 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain M residue 28 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.118441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.077757 restraints weight = 3109.330| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.78 r_work: 0.3088 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2965 Z= 0.170 Angle : 0.450 4.270 4015 Z= 0.252 Chirality : 0.045 0.138 465 Planarity : 0.001 0.006 525 Dihedral : 4.791 18.260 405 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.56 % Allowed : 8.12 % Favored : 90.31 % 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: -3.06 (0.30), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 18 PHE 0.012 0.001 PHE I 23 TYR 0.006 0.001 TYR D 37 ARG 0.001 0.000 ARG F 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1770.84 seconds wall clock time: 31 minutes 11.35 seconds (1871.35 seconds total)