Starting phenix.real_space_refine on Mon Sep 23 13:09:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az2_15730/09_2024/8az2_15730.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az2_15730/09_2024/8az2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az2_15730/09_2024/8az2_15730.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az2_15730/09_2024/8az2_15730.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az2_15730/09_2024/8az2_15730.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az2_15730/09_2024/8az2_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-5461/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: 2.36, per 1000 atoms: 0.80 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: 0.75 Conformation dependent library (CDL) restraints added in 308.4 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: 0.56 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: 0.73 Time building geometry restraints manager: 0.86 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.530 Find NCS groups from input model: 0.160 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.930 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.301 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: 0.0864 time to fit residues: 2.4644 Evaluate side-chains 14 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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: 0.9980 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: 3.1988 ------------------------------------------------------------------------------- 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 14 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: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2050 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= 0.349 Angle : 0.498 3.267 4015 Z= 0.281 Chirality : 0.046 0.134 465 Planarity : 0.002 0.010 525 Dihedral : 4.977 19.650 405 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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 0.012 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 14 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 10 time to evaluate : 0.291 Fit side-chains REVERT: D 31 ASN cc_start: 0.8555 (t0) cc_final: 0.8229 (t0) outliers start: 4 outliers final: 4 residues processed: 14 average time/residue: 0.0766 time to fit residues: 1.8892 Evaluate side-chains 14 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 10 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: 8.9990 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 14 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: 0.8154 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2965 Z= 0.159 Angle : 0.421 3.087 4015 Z= 0.235 Chirality : 0.044 0.130 465 Planarity : 0.001 0.007 525 Dihedral : 4.339 17.846 405 Min Nonbonded Distance : 2.674 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.25 % Allowed : 3.12 % Favored : 95.62 % 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: -2.84 (0.30), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS M 18 PHE 0.008 0.001 PHE L 23 TYR 0.007 0.001 TYR D 37 ARG 0.000 0.000 ARG C 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 fitting. rotamer outliers: 4 poor density : 10 time to evaluate : 0.344 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 14 average time/residue: 0.0802 time to fit residues: 1.9474 Evaluate side-chains 13 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 9 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 3 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 28 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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: 0.8207 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2965 Z= 0.278 Angle : 0.454 3.330 4015 Z= 0.258 Chirality : 0.045 0.130 465 Planarity : 0.002 0.013 525 Dihedral : 4.797 21.174 405 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.25 % Allowed : 6.25 % Favored : 92.50 % 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: -2.94 (0.30), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 18 PHE 0.010 0.001 PHE I 23 TYR 0.009 0.001 TYR D 37 ARG 0.001 0.000 ARG L 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 14 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 10 time to evaluate : 0.298 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 14 average time/residue: 0.0842 time to fit residues: 1.9932 Evaluate side-chains 14 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 10 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 21 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 2965 Z= 0.470 Angle : 0.519 3.715 4015 Z= 0.300 Chirality : 0.047 0.131 465 Planarity : 0.003 0.016 525 Dihedral : 5.289 21.527 405 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % 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: -3.15 (0.29), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.22), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS J 18 PHE 0.010 0.002 PHE A 15 TYR 0.009 0.002 TYR D 37 ARG 0.001 0.000 ARG O 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 18 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 14 time to evaluate : 0.312 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 18 average time/residue: 0.0822 time to fit residues: 2.4358 Evaluate side-chains 18 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 14 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 7 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 21 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2965 Z= 0.194 Angle : 0.435 3.828 4015 Z= 0.245 Chirality : 0.045 0.135 465 Planarity : 0.001 0.007 525 Dihedral : 4.577 18.571 405 Min Nonbonded Distance : 2.503 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: -3.11 (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 0.004 0.001 HIS J 18 PHE 0.010 0.001 PHE C 23 TYR 0.007 0.001 TYR D 37 ARG 0.000 0.000 ARG G 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 18 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 14 time to evaluate : 0.348 Fit side-chains REVERT: O 37 TYR cc_start: 0.8946 (m-80) cc_final: 0.8598 (m-80) outliers start: 4 outliers final: 4 residues processed: 18 average time/residue: 0.0802 time to fit residues: 2.3830 Evaluate side-chains 18 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 14 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 16 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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: 0.8259 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2965 Z= 0.362 Angle : 0.482 3.902 4015 Z= 0.276 Chirality : 0.046 0.134 465 Planarity : 0.002 0.012 525 Dihedral : 5.046 20.702 405 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % 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: -3.14 (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 0.007 0.001 HIS J 18 PHE 0.016 0.002 PHE O 23 TYR 0.008 0.001 TYR D 37 ARG 0.001 0.000 ARG C 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 19 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 15 time to evaluate : 0.284 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 19 average time/residue: 0.0823 time to fit residues: 2.4731 Evaluate side-chains 19 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 15 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 2 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2965 Z= 0.275 Angle : 0.456 3.903 4015 Z= 0.260 Chirality : 0.045 0.135 465 Planarity : 0.002 0.010 525 Dihedral : 4.813 19.067 405 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % 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: -3.07 (0.30), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS J 18 PHE 0.018 0.001 PHE O 23 TYR 0.007 0.001 TYR D 37 ARG 0.000 0.000 ARG I 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 18 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 14 time to evaluate : 0.302 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 18 average time/residue: 0.0792 time to fit residues: 2.3362 Evaluate side-chains 18 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 14 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 28 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2965 Z= 0.166 Angle : 0.424 3.905 4015 Z= 0.239 Chirality : 0.044 0.135 465 Planarity : 0.001 0.008 525 Dihedral : 4.377 17.881 405 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.56 % Allowed : 7.50 % 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: -2.94 (0.31), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 18 PHE 0.019 0.001 PHE O 23 TYR 0.006 0.001 TYR D 37 ARG 0.000 0.000 ARG L 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 18 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 13 time to evaluate : 0.314 Fit side-chains REVERT: O 37 TYR cc_start: 0.8891 (m-80) cc_final: 0.8533 (m-80) outliers start: 5 outliers final: 4 residues processed: 17 average time/residue: 0.0836 time to fit residues: 2.3262 Evaluate side-chains 16 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 12 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 7 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 2965 Z= 0.400 Angle : 0.493 3.864 4015 Z= 0.286 Chirality : 0.046 0.138 465 Planarity : 0.003 0.017 525 Dihedral : 5.141 20.670 405 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % 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: -2.96 (0.31), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS J 18 PHE 0.018 0.002 PHE O 23 TYR 0.007 0.001 TYR D 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 20 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 15 time to evaluate : 0.284 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 19 average time/residue: 0.0751 time to fit residues: 2.3104 Evaluate side-chains 19 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 15 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 27 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN O 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.114482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.072835 restraints weight = 3249.793| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.79 r_work: 0.2997 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 2965 Z= 0.464 Angle : 0.528 4.013 4015 Z= 0.307 Chirality : 0.047 0.136 465 Planarity : 0.003 0.019 525 Dihedral : 5.440 20.427 405 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % 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: -2.99 (0.30), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS J 18 PHE 0.017 0.002 PHE O 23 TYR 0.008 0.002 TYR J 37 ARG 0.001 0.000 ARG L 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 961.86 seconds wall clock time: 17 minutes 48.55 seconds (1068.55 seconds total)