Starting phenix.real_space_refine on Mon Sep 23 23:34:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q65_13852/09_2024/7q65_13852.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q65_13852/09_2024/7q65_13852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q65_13852/09_2024/7q65_13852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q65_13852/09_2024/7q65_13852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q65_13852/09_2024/7q65_13852.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q65_13852/09_2024/7q65_13852.cif" } resolution = 3.32 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= 0.001 sd= 0.008 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 3806 2.51 5 N 1056 2.21 5 O 1342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6204 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "B" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Restraints were copied for chains: C, E, G, I, K, M, O, Q, S, U, D, F, H, J, L, N, P, R, T, V Time building chain proxies: 2.25, per 1000 atoms: 0.36 Number of scatterers: 6204 At special positions: 0 Unit cell: (79.8, 65.1, 77.7, 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 1342 8.00 N 1056 7.00 C 3806 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=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 777.9 milliseconds 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1496 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 103 removed outlier: 6.526A pdb=" N THR A 99 " --> pdb=" O SER C 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE C 102 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU A 101 " --> pdb=" O PHE C 102 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR C 99 " --> pdb=" O SER E 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE E 102 " --> pdb=" O THR C 99 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU C 101 " --> pdb=" O PHE E 102 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR E 99 " --> pdb=" O SER G 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE G 102 " --> pdb=" O THR E 99 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU E 101 " --> pdb=" O PHE G 102 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR G 99 " --> pdb=" O SER I 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE I 102 " --> pdb=" O THR G 99 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU G 101 " --> pdb=" O PHE I 102 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR I 99 " --> pdb=" O SER K 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE K 102 " --> pdb=" O THR I 99 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU I 101 " --> pdb=" O PHE K 102 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR K 99 " --> pdb=" O SER M 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE M 102 " --> pdb=" O THR K 99 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU K 101 " --> pdb=" O PHE M 102 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR M 99 " --> pdb=" O SER O 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE O 102 " --> pdb=" O THR M 99 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU M 101 " --> pdb=" O PHE O 102 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR O 99 " --> pdb=" O SER Q 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE Q 102 " --> pdb=" O THR O 99 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU O 101 " --> pdb=" O PHE Q 102 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR Q 99 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N PHE S 102 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU Q 101 " --> pdb=" O PHE S 102 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR S 99 " --> pdb=" O SER U 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE U 102 " --> pdb=" O THR S 99 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU S 101 " --> pdb=" O PHE U 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 106 through 107 Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 122 removed outlier: 6.805A pdb=" N GLY C 121 " --> pdb=" O PHE A 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY E 121 " --> pdb=" O PHE C 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY G 121 " --> pdb=" O PHE E 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY I 121 " --> pdb=" O PHE G 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY K 121 " --> pdb=" O PHE I 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY M 121 " --> pdb=" O PHE K 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY O 121 " --> pdb=" O PHE M 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY Q 121 " --> pdb=" O PHE O 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY S 121 " --> pdb=" O PHE Q 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY U 121 " --> pdb=" O PHE S 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 88 through 89 Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 101 removed outlier: 6.544A pdb=" N SER B 100 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER D 100 " --> pdb=" O LEU F 101 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER F 100 " --> pdb=" O LEU H 101 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER H 100 " --> pdb=" O LEU J 101 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER J 100 " --> pdb=" O LEU L 101 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER L 100 " --> pdb=" O LEU N 101 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER N 100 " --> pdb=" O LEU P 101 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER P 100 " --> pdb=" O LEU R 101 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER R 100 " --> pdb=" O LEU T 101 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER T 100 " --> pdb=" O LEU V 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 104 through 106 removed outlier: 6.323A pdb=" N SER B 104 " --> pdb=" O GLN D 105 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER D 104 " --> pdb=" O GLN F 105 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER F 104 " --> pdb=" O GLN H 105 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N SER H 104 " --> pdb=" O GLN J 105 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER J 104 " --> pdb=" O GLN L 105 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER L 104 " --> pdb=" O GLN N 105 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER N 104 " --> pdb=" O GLN P 105 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER P 104 " --> pdb=" O GLN R 105 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER R 104 " --> pdb=" O GLN T 105 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER T 104 " --> pdb=" O GLN V 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 111 through 112 Processing sheet with id=AA8, first strand: chain 'B' and resid 118 through 123 removed outlier: 6.843A pdb=" N ASN D 119 " --> pdb=" O GLY B 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE B 120 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY D 121 " --> pdb=" O PHE B 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN F 119 " --> pdb=" O GLY D 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE D 120 " --> pdb=" O ASN F 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY F 121 " --> pdb=" O PHE D 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN H 119 " --> pdb=" O GLY F 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE F 120 " --> pdb=" O ASN H 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY H 121 " --> pdb=" O PHE F 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN J 119 " --> pdb=" O GLY H 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE H 120 " --> pdb=" O ASN J 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY J 121 " --> pdb=" O PHE H 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN L 119 " --> pdb=" O GLY J 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE J 120 " --> pdb=" O ASN L 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY L 121 " --> pdb=" O PHE J 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN N 119 " --> pdb=" O GLY L 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE L 120 " --> pdb=" O ASN N 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY N 121 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN P 119 " --> pdb=" O GLY N 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE N 120 " --> pdb=" O ASN P 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY P 121 " --> pdb=" O PHE N 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN R 119 " --> pdb=" O GLY P 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE P 120 " --> pdb=" O ASN R 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY R 121 " --> pdb=" O PHE P 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN T 119 " --> pdb=" O GLY R 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE R 120 " --> pdb=" O ASN T 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY T 121 " --> pdb=" O PHE R 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN V 119 " --> pdb=" O GLY T 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE T 120 " --> pdb=" O ASN V 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY V 121 " --> pdb=" O PHE T 120 " (cutoff:3.500A) 60 hydrogen bonds defined for protein. 180 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.64 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.28: 1034 1.28 - 1.35: 1023 1.35 - 1.42: 766 1.42 - 1.49: 1544 1.49 - 1.57: 1947 Bond restraints: 6314 Sorted by residual: bond pdb=" CA ASN S 106 " pdb=" CB ASN S 106 " ideal model delta sigma weight residual 1.527 1.482 0.045 1.75e-02 3.27e+03 6.56e+00 bond pdb=" CA ASN U 106 " pdb=" CB ASN U 106 " ideal model delta sigma weight residual 1.527 1.482 0.045 1.75e-02 3.27e+03 6.49e+00 bond pdb=" CA ASN Q 106 " pdb=" CB ASN Q 106 " ideal model delta sigma weight residual 1.527 1.482 0.045 1.75e-02 3.27e+03 6.48e+00 bond pdb=" CA ASN M 106 " pdb=" CB ASN M 106 " ideal model delta sigma weight residual 1.527 1.482 0.044 1.75e-02 3.27e+03 6.43e+00 bond pdb=" CA ASN C 106 " pdb=" CB ASN C 106 " ideal model delta sigma weight residual 1.527 1.482 0.044 1.75e-02 3.27e+03 6.42e+00 ... (remaining 6309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 7559 2.02 - 4.04: 724 4.04 - 6.07: 154 6.07 - 8.09: 88 8.09 - 10.11: 33 Bond angle restraints: 8558 Sorted by residual: angle pdb=" CA ASN N 106 " pdb=" CB ASN N 106 " pdb=" CG ASN N 106 " ideal model delta sigma weight residual 112.60 118.08 -5.48 1.00e+00 1.00e+00 3.00e+01 angle pdb=" CA ASN V 106 " pdb=" CB ASN V 106 " pdb=" CG ASN V 106 " ideal model delta sigma weight residual 112.60 118.06 -5.46 1.00e+00 1.00e+00 2.99e+01 angle pdb=" CA ASN P 106 " pdb=" CB ASN P 106 " pdb=" CG ASN P 106 " ideal model delta sigma weight residual 112.60 118.06 -5.46 1.00e+00 1.00e+00 2.98e+01 angle pdb=" CA ASN H 106 " pdb=" CB ASN H 106 " pdb=" CG ASN H 106 " ideal model delta sigma weight residual 112.60 118.06 -5.46 1.00e+00 1.00e+00 2.98e+01 angle pdb=" CA ASN L 106 " pdb=" CB ASN L 106 " pdb=" CG ASN L 106 " ideal model delta sigma weight residual 112.60 118.05 -5.45 1.00e+00 1.00e+00 2.97e+01 ... (remaining 8553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.47: 2641 7.47 - 14.94: 604 14.94 - 22.40: 143 22.40 - 29.87: 66 29.87 - 37.34: 22 Dihedral angle restraints: 3476 sinusoidal: 1122 harmonic: 2354 Sorted by residual: dihedral pdb=" CA THR K 85 " pdb=" C THR K 85 " pdb=" N GLY K 86 " pdb=" CA GLY K 86 " ideal model delta harmonic sigma weight residual -180.00 -154.29 -25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA THR I 85 " pdb=" C THR I 85 " pdb=" N GLY I 86 " pdb=" CA GLY I 86 " ideal model delta harmonic sigma weight residual -180.00 -154.29 -25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA THR G 85 " pdb=" C THR G 85 " pdb=" N GLY G 86 " pdb=" CA GLY G 86 " ideal model delta harmonic sigma weight residual -180.00 -154.29 -25.71 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 3473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 654 0.069 - 0.139: 248 0.139 - 0.208: 22 0.208 - 0.277: 33 0.277 - 0.347: 33 Chirality restraints: 990 Sorted by residual: chirality pdb=" CB THR O 94 " pdb=" CA THR O 94 " pdb=" OG1 THR O 94 " pdb=" CG2 THR O 94 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CB THR E 94 " pdb=" CA THR E 94 " pdb=" OG1 THR E 94 " pdb=" CG2 THR E 94 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CB THR S 94 " pdb=" CA THR S 94 " pdb=" OG1 THR S 94 " pdb=" CG2 THR S 94 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 987 not shown) Planarity restraints: 1144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN N 106 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C ASN N 106 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN N 106 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN N 107 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 106 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C ASN F 106 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN F 106 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN F 107 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN L 106 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C ASN L 106 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN L 106 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN L 107 " -0.012 2.00e-02 2.50e+03 ... (remaining 1141 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 576 2.71 - 3.26: 6253 3.26 - 3.80: 12009 3.80 - 4.35: 14019 4.35 - 4.90: 28813 Nonbonded interactions: 61670 Sorted by model distance: nonbonded pdb=" O GLY E 93 " pdb=" OG SER G 96 " model vdw 2.159 3.040 nonbonded pdb=" O GLY O 93 " pdb=" OG SER Q 96 " model vdw 2.159 3.040 nonbonded pdb=" O GLY Q 93 " pdb=" OG SER S 96 " model vdw 2.159 3.040 nonbonded pdb=" O GLY K 93 " pdb=" OG SER M 96 " model vdw 2.159 3.040 nonbonded pdb=" O GLY S 93 " pdb=" OG SER U 96 " model vdw 2.159 3.040 ... (remaining 61665 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } 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: 0.650 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.290 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 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 : 0.016 0.073 6314 Z= 1.048 Angle : 1.561 10.109 8558 Z= 0.897 Chirality : 0.097 0.347 990 Planarity : 0.006 0.021 1144 Dihedral : 10.100 37.337 1980 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 8.33 % Allowed : 3.18 % Favored : 88.48 % 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: -5.74 (0.13), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.37 (0.10), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.005 PHE V 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 217 time to evaluate : 0.644 Fit side-chains REVERT: A 89 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8661 (p0) REVERT: A 113 LYS cc_start: 0.8860 (ptpt) cc_final: 0.8125 (mmpt) REVERT: C 89 ASN cc_start: 0.8892 (OUTLIER) cc_final: 0.8627 (p0) REVERT: H 124 THR cc_start: 0.9334 (OUTLIER) cc_final: 0.9127 (p) REVERT: L 112 ASN cc_start: 0.8513 (t0) cc_final: 0.8289 (t0) REVERT: L 124 THR cc_start: 0.9267 (OUTLIER) cc_final: 0.9024 (p) REVERT: M 115 THR cc_start: 0.8610 (p) cc_final: 0.8185 (m) REVERT: N 104 SER cc_start: 0.8834 (m) cc_final: 0.8615 (m) REVERT: N 112 ASN cc_start: 0.8251 (t0) cc_final: 0.7984 (t0) REVERT: O 115 THR cc_start: 0.8657 (p) cc_final: 0.8405 (m) REVERT: R 87 THR cc_start: 0.9106 (t) cc_final: 0.8904 (m) REVERT: S 89 ASN cc_start: 0.8933 (OUTLIER) cc_final: 0.8672 (p0) REVERT: U 89 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8521 (p0) REVERT: U 113 LYS cc_start: 0.8978 (ptpt) cc_final: 0.8593 (ptpp) outliers start: 55 outliers final: 34 residues processed: 254 average time/residue: 0.1363 time to fit residues: 48.0240 Evaluate side-chains 194 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 154 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 89 ASN Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain L residue 124 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 91 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 89 ASN Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 89 ASN Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 91 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** H 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 106 ASN ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6314 Z= 0.203 Angle : 0.663 6.644 8558 Z= 0.349 Chirality : 0.033 0.136 990 Planarity : 0.004 0.025 1144 Dihedral : 8.867 57.384 917 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 8.79 % Allowed : 11.06 % Favored : 80.15 % 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: -5.66 (0.14), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.30 (0.10), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.032 0.001 PHE V 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 197 time to evaluate : 0.664 Fit side-chains REVERT: A 113 LYS cc_start: 0.8825 (ptpt) cc_final: 0.7691 (mmmt) REVERT: E 115 THR cc_start: 0.8486 (t) cc_final: 0.8205 (m) REVERT: J 106 ASN cc_start: 0.8647 (OUTLIER) cc_final: 0.8443 (p0) REVERT: K 113 LYS cc_start: 0.8694 (ptpp) cc_final: 0.8460 (mttm) REVERT: L 124 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8812 (p) REVERT: M 87 THR cc_start: 0.8215 (OUTLIER) cc_final: 0.7830 (t) REVERT: N 106 ASN cc_start: 0.8472 (OUTLIER) cc_final: 0.8220 (p0) REVERT: S 113 LYS cc_start: 0.8620 (ptpp) cc_final: 0.8327 (mttm) REVERT: T 111 GLN cc_start: 0.7807 (pt0) cc_final: 0.7373 (mt0) outliers start: 58 outliers final: 35 residues processed: 228 average time/residue: 0.1277 time to fit residues: 41.2915 Evaluate side-chains 186 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 147 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 124 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 91 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 91 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 64 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 ASN ** L 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 GLN ** T 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 89 ASN ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6314 Z= 0.294 Angle : 0.678 7.099 8558 Z= 0.353 Chirality : 0.034 0.197 990 Planarity : 0.003 0.020 1144 Dihedral : 8.083 59.401 892 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 11.52 % Allowed : 13.03 % Favored : 75.45 % 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: -5.66 (0.14), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.31 (0.10), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.001 PHE V 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 163 time to evaluate : 0.705 Fit side-chains REVERT: A 113 LYS cc_start: 0.8954 (ptpt) cc_final: 0.7768 (mmpt) REVERT: C 91 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8815 (tp) REVERT: G 91 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8695 (tp) REVERT: K 91 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8695 (tt) REVERT: K 115 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8610 (m) REVERT: L 124 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8886 (p) REVERT: R 87 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8677 (m) REVERT: R 106 ASN cc_start: 0.8466 (p0) cc_final: 0.8135 (p0) REVERT: S 113 LYS cc_start: 0.8790 (ptpp) cc_final: 0.8452 (mttm) outliers start: 76 outliers final: 56 residues processed: 206 average time/residue: 0.1218 time to fit residues: 36.3762 Evaluate side-chains 200 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 138 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 124 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 97 THR Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 123 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 GLN I 89 ASN ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN ** L 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 ASN ** T 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 89 ASN ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.048 6314 Z= 0.576 Angle : 0.791 8.060 8558 Z= 0.419 Chirality : 0.042 0.171 990 Planarity : 0.004 0.027 1144 Dihedral : 7.363 49.836 884 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 13.48 % Allowed : 12.88 % Favored : 73.64 % 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: -5.41 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.12 (0.11), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.002 PHE V 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 141 time to evaluate : 0.660 Fit side-chains REVERT: A 113 LYS cc_start: 0.9026 (ptpt) cc_final: 0.7873 (mmpt) REVERT: J 112 ASN cc_start: 0.8362 (t0) cc_final: 0.8076 (t0) REVERT: R 87 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8704 (m) REVERT: R 106 ASN cc_start: 0.8505 (p0) cc_final: 0.8255 (p0) outliers start: 89 outliers final: 75 residues processed: 190 average time/residue: 0.1216 time to fit residues: 33.3556 Evaluate side-chains 204 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 128 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 97 THR Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 97 THR Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 123 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN B 112 ASN ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 ASN ** L 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 ASN ** P 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 GLN ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6314 Z= 0.183 Angle : 0.627 7.445 8558 Z= 0.319 Chirality : 0.032 0.129 990 Planarity : 0.003 0.018 1144 Dihedral : 5.833 46.880 875 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 8.48 % Allowed : 18.79 % Favored : 72.73 % 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: -5.48 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.17 (0.11), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.001 PHE V 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 157 time to evaluate : 0.765 Fit side-chains REVERT: A 113 LYS cc_start: 0.8813 (ptpt) cc_final: 0.7446 (mmmt) REVERT: D 106 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8135 (p0) REVERT: K 113 LYS cc_start: 0.8785 (ptpp) cc_final: 0.8576 (mttp) REVERT: R 87 THR cc_start: 0.8828 (t) cc_final: 0.8552 (m) REVERT: R 106 ASN cc_start: 0.8416 (p0) cc_final: 0.8087 (p0) outliers start: 56 outliers final: 40 residues processed: 191 average time/residue: 0.1381 time to fit residues: 37.5941 Evaluate side-chains 174 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 133 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 104 SER Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 123 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 39 optimal weight: 0.0370 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 overall best weight: 2.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 GLN O 89 ASN O 105 GLN ** P 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6314 Z= 0.317 Angle : 0.656 6.993 8558 Z= 0.338 Chirality : 0.034 0.115 990 Planarity : 0.003 0.022 1144 Dihedral : 5.973 50.672 874 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 9.85 % Allowed : 17.42 % Favored : 72.73 % 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: -5.39 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.10 (0.11), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.001 PHE V 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 139 time to evaluate : 0.513 Fit side-chains REVERT: A 113 LYS cc_start: 0.8945 (ptpt) cc_final: 0.7640 (mmmt) REVERT: R 87 THR cc_start: 0.8832 (t) cc_final: 0.8567 (m) REVERT: R 106 ASN cc_start: 0.8475 (p0) cc_final: 0.8205 (p0) REVERT: T 104 SER cc_start: 0.8513 (p) cc_final: 0.8293 (p) outliers start: 65 outliers final: 57 residues processed: 172 average time/residue: 0.0999 time to fit residues: 25.2960 Evaluate side-chains 188 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 131 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 123 SER Chi-restraints excluded: chain V residue 106 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 53 optimal weight: 0.0970 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 ASN ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 ASN ** L 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 GLN O 89 ASN P 107 ASN ** Q 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 107 ASN ** T 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6314 Z= 0.191 Angle : 0.593 6.627 8558 Z= 0.302 Chirality : 0.031 0.111 990 Planarity : 0.002 0.017 1144 Dihedral : 5.586 55.205 873 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 8.33 % Allowed : 18.64 % Favored : 73.03 % 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: -5.40 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.11 (0.11), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.001 PHE V 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 139 time to evaluate : 0.694 Fit side-chains REVERT: A 113 LYS cc_start: 0.8822 (ptpt) cc_final: 0.7568 (mmmt) REVERT: D 106 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8137 (p0) REVERT: N 106 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.7705 (p0) REVERT: R 106 ASN cc_start: 0.8416 (p0) cc_final: 0.8140 (p0) outliers start: 55 outliers final: 48 residues processed: 173 average time/residue: 0.1176 time to fit residues: 30.0975 Evaluate side-chains 177 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 127 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 123 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 GLN ** Q 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 GLN ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 6314 Z= 0.464 Angle : 0.696 7.472 8558 Z= 0.367 Chirality : 0.037 0.122 990 Planarity : 0.003 0.023 1144 Dihedral : 6.156 48.961 871 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 9.39 % Allowed : 18.03 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.24 (0.16), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.12), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.002 PHE V 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 131 time to evaluate : 0.667 Fit side-chains REVERT: A 112 ASN cc_start: 0.8238 (t0) cc_final: 0.8035 (t0) REVERT: A 113 LYS cc_start: 0.8991 (ptpt) cc_final: 0.7674 (mmmt) REVERT: R 106 ASN cc_start: 0.8504 (p0) cc_final: 0.8212 (p0) REVERT: T 111 GLN cc_start: 0.8097 (mt0) cc_final: 0.7875 (mt0) outliers start: 62 outliers final: 58 residues processed: 165 average time/residue: 0.1127 time to fit residues: 27.5235 Evaluate side-chains 184 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 126 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 123 SER Chi-restraints excluded: chain V residue 106 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 GLN ** P 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6314 Z= 0.252 Angle : 0.618 7.015 8558 Z= 0.320 Chirality : 0.032 0.110 990 Planarity : 0.003 0.020 1144 Dihedral : 5.808 52.508 871 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 8.79 % Allowed : 18.94 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.26 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.12), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.001 PHE V 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 136 time to evaluate : 0.665 Fit side-chains REVERT: A 113 LYS cc_start: 0.8921 (ptpt) cc_final: 0.7639 (mmmt) REVERT: B 101 LEU cc_start: 0.8503 (mp) cc_final: 0.8283 (mp) REVERT: R 87 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8503 (m) REVERT: R 106 ASN cc_start: 0.8470 (p0) cc_final: 0.8176 (p0) outliers start: 58 outliers final: 54 residues processed: 170 average time/residue: 0.1116 time to fit residues: 28.3585 Evaluate side-chains 186 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 131 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 123 SER Chi-restraints excluded: chain V residue 106 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 87 optimal weight: 0.4980 chunk 80 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 GLN ** Q 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 GLN ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6314 Z= 0.172 Angle : 0.579 6.834 8558 Z= 0.294 Chirality : 0.030 0.104 990 Planarity : 0.002 0.018 1144 Dihedral : 5.498 59.875 871 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 6.82 % Allowed : 21.06 % Favored : 72.12 % 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: -5.31 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.11), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.001 PHE V 117 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 137 time to evaluate : 0.606 Fit side-chains REVERT: A 113 LYS cc_start: 0.8771 (ptpt) cc_final: 0.7552 (mmmt) REVERT: R 106 ASN cc_start: 0.8446 (p0) cc_final: 0.8171 (p0) outliers start: 45 outliers final: 42 residues processed: 165 average time/residue: 0.1090 time to fit residues: 26.7726 Evaluate side-chains 170 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 128 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 123 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 3 optimal weight: 0.0040 overall best weight: 1.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 106 ASN ** T 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 GLN ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.090368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.074159 restraints weight = 10075.339| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.38 r_work: 0.3183 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6314 Z= 0.266 Angle : 0.610 7.291 8558 Z= 0.315 Chirality : 0.032 0.108 990 Planarity : 0.002 0.019 1144 Dihedral : 5.624 49.833 871 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 7.73 % Allowed : 20.45 % Favored : 71.82 % 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: -5.24 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.12), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.001 PHE V 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1647.31 seconds wall clock time: 39 minutes 18.28 seconds (2358.28 seconds total)