Starting phenix.real_space_refine on Sat Dec 9 23:12:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6j_5925/12_2023/3j6j_5925.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6j_5925/12_2023/3j6j_5925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6j_5925/12_2023/3j6j_5925.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6j_5925/12_2023/3j6j_5925.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6j_5925/12_2023/3j6j_5925.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6j_5925/12_2023/3j6j_5925.pdb" } resolution = 3.64 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= 0.032 sd= 0.127 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6344 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 4040 2.51 5 N 1088 2.21 5 O 1168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 5": "OE1" <-> "OE2" Residue "D GLU 26": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6344 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "C" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "D" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "E" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "G" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "I" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "L" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Time building chain proxies: 3.81, per 1000 atoms: 0.60 Number of scatterers: 6344 At special positions: 0 Unit cell: (99, 96.8, 80.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1168 8.00 N 1088 7.00 C 4040 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.2 seconds 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 88.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 1 through 15 Processing helix chain 'A' and resid 15 through 20 removed outlier: 4.052A pdb=" N PHE A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N CYS A 20 " --> pdb=" O PHE A 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 15 through 20' Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 37 through 50 Processing helix chain 'A' and resid 50 through 63 removed outlier: 3.686A pdb=" N HIS A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 79 removed outlier: 3.651A pdb=" N TYR A 71 " --> pdb=" O GLY A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'B' and resid 16 through 20 removed outlier: 3.903A pdb=" N CYS B 20 " --> pdb=" O SER B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 28 Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 35 through 50 removed outlier: 4.101A pdb=" N ASP B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B 41 " --> pdb=" O ARG B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 63 removed outlier: 3.529A pdb=" N TRP B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS B 57 " --> pdb=" O ASP B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 79 removed outlier: 3.660A pdb=" N TYR B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 94 removed outlier: 3.673A pdb=" N SER B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 15 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 23 through 28 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 35 through 50 removed outlier: 3.705A pdb=" N ASP C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 63 removed outlier: 3.660A pdb=" N HIS C 57 " --> pdb=" O ASP C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 79 removed outlier: 3.600A pdb=" N TYR C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 94 Processing helix chain 'D' and resid 2 through 15 Processing helix chain 'D' and resid 15 through 20 removed outlier: 3.667A pdb=" N PHE D 19 " --> pdb=" O ASN D 15 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS D 20 " --> pdb=" O PHE D 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 15 through 20' Processing helix chain 'D' and resid 23 through 28 Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 35 through 50 removed outlier: 4.090A pdb=" N ASP D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 63 removed outlier: 3.502A pdb=" N TRP D 56 " --> pdb=" O ARG D 52 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS D 57 " --> pdb=" O ASP D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 79 Processing helix chain 'D' and resid 81 through 94 Processing helix chain 'E' and resid 2 through 15 Processing helix chain 'E' and resid 15 through 20 removed outlier: 3.953A pdb=" N PHE E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N CYS E 20 " --> pdb=" O PHE E 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 15 through 20' Processing helix chain 'E' and resid 23 through 28 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 35 through 50 removed outlier: 4.123A pdb=" N ASP E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 63 removed outlier: 3.865A pdb=" N TRP E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 79 removed outlier: 3.836A pdb=" N TYR E 71 " --> pdb=" O GLY E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 94 Processing helix chain 'G' and resid 2 through 15 Processing helix chain 'G' and resid 15 through 20 removed outlier: 3.834A pdb=" N PHE G 19 " --> pdb=" O ASN G 15 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS G 20 " --> pdb=" O PHE G 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 15 through 20' Processing helix chain 'G' and resid 23 through 28 Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 35 through 50 removed outlier: 3.985A pdb=" N ASP G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 63 removed outlier: 3.666A pdb=" N TRP G 56 " --> pdb=" O ARG G 52 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N HIS G 57 " --> pdb=" O ASP G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 79 removed outlier: 3.537A pdb=" N TYR G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 95 removed outlier: 3.613A pdb=" N TYR G 95 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 15 Processing helix chain 'I' and resid 15 through 20 removed outlier: 3.668A pdb=" N PHE I 19 " --> pdb=" O ASN I 15 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS I 20 " --> pdb=" O PHE I 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 15 through 20' Processing helix chain 'I' and resid 23 through 28 Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 35 through 50 removed outlier: 3.889A pdb=" N ASP I 40 " --> pdb=" O ALA I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 63 removed outlier: 3.992A pdb=" N TRP I 56 " --> pdb=" O ARG I 52 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS I 57 " --> pdb=" O ASP I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 79 removed outlier: 3.655A pdb=" N TYR I 71 " --> pdb=" O GLY I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 94 Processing helix chain 'L' and resid 2 through 15 Processing helix chain 'L' and resid 15 through 20 removed outlier: 3.564A pdb=" N PHE L 19 " --> pdb=" O ASN L 15 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS L 20 " --> pdb=" O PHE L 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 15 through 20' Processing helix chain 'L' and resid 23 through 28 Processing helix chain 'L' and resid 35 through 50 removed outlier: 3.997A pdb=" N ASP L 40 " --> pdb=" O ALA L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 63 removed outlier: 3.570A pdb=" N TRP L 56 " --> pdb=" O ARG L 52 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS L 57 " --> pdb=" O ASP L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 79 removed outlier: 3.710A pdb=" N TYR L 71 " --> pdb=" O GLY L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 94 396 hydrogen bonds defined for protein. 1185 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: 1.66 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2016 1.33 - 1.46: 1206 1.46 - 1.58: 3218 1.58 - 1.70: 0 1.70 - 1.82: 56 Bond restraints: 6496 Sorted by residual: bond pdb=" C LEU L 28 " pdb=" N PRO L 29 " ideal model delta sigma weight residual 1.336 1.419 -0.083 1.20e-02 6.94e+03 4.81e+01 bond pdb=" N PRO L 29 " pdb=" CD PRO L 29 " ideal model delta sigma weight residual 1.473 1.517 -0.044 1.40e-02 5.10e+03 9.93e+00 bond pdb=" C ILE D 12 " pdb=" O ILE D 12 " ideal model delta sigma weight residual 1.237 1.212 0.025 1.13e-02 7.83e+03 4.80e+00 bond pdb=" C ILE B 12 " pdb=" O ILE B 12 " ideal model delta sigma weight residual 1.237 1.212 0.025 1.13e-02 7.83e+03 4.80e+00 bond pdb=" N CYS D 20 " pdb=" CA CYS D 20 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.62e+00 ... (remaining 6491 not shown) Histogram of bond angle deviations from ideal: 97.09 - 106.88: 198 106.88 - 116.66: 4334 116.66 - 126.45: 4219 126.45 - 136.23: 88 136.23 - 146.02: 1 Bond angle restraints: 8840 Sorted by residual: angle pdb=" N ARG A 37 " pdb=" CA ARG A 37 " pdb=" C ARG A 37 " ideal model delta sigma weight residual 111.36 119.53 -8.17 1.09e+00 8.42e-01 5.61e+01 angle pdb=" C LEU D 31 " pdb=" N PRO D 32 " pdb=" CA PRO D 32 " ideal model delta sigma weight residual 119.87 127.63 -7.76 1.04e+00 9.25e-01 5.57e+01 angle pdb=" N ASN A 51 " pdb=" CA ASN A 51 " pdb=" C ASN A 51 " ideal model delta sigma weight residual 111.03 118.81 -7.78 1.11e+00 8.12e-01 4.91e+01 angle pdb=" CA PRO L 29 " pdb=" N PRO L 29 " pdb=" CD PRO L 29 " ideal model delta sigma weight residual 112.00 102.49 9.51 1.40e+00 5.10e-01 4.61e+01 angle pdb=" C LEU L 28 " pdb=" N PRO L 29 " pdb=" CA PRO L 29 " ideal model delta sigma weight residual 118.85 111.48 7.37 1.09e+00 8.42e-01 4.57e+01 ... (remaining 8835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 3418 16.97 - 33.94: 279 33.94 - 50.91: 111 50.91 - 67.88: 45 67.88 - 84.85: 3 Dihedral angle restraints: 3856 sinusoidal: 1536 harmonic: 2320 Sorted by residual: dihedral pdb=" CG ARG I 64 " pdb=" CD ARG I 64 " pdb=" NE ARG I 64 " pdb=" CZ ARG I 64 " ideal model delta sinusoidal sigma weight residual -90.00 -10.80 -79.20 2 1.50e+01 4.44e-03 2.06e+01 dihedral pdb=" CG ARG G 64 " pdb=" CD ARG G 64 " pdb=" NE ARG G 64 " pdb=" CZ ARG G 64 " ideal model delta sinusoidal sigma weight residual -90.00 -12.28 -77.72 2 1.50e+01 4.44e-03 2.04e+01 dihedral pdb=" CA LEU I 48 " pdb=" C LEU I 48 " pdb=" N SER I 49 " pdb=" CA SER I 49 " ideal model delta harmonic sigma weight residual -180.00 -163.64 -16.36 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 3853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 770 0.069 - 0.137: 170 0.137 - 0.206: 23 0.206 - 0.275: 4 0.275 - 0.343: 1 Chirality restraints: 968 Sorted by residual: chirality pdb=" CA LEU L 28 " pdb=" N LEU L 28 " pdb=" C LEU L 28 " pdb=" CB LEU L 28 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA ARG A 37 " pdb=" N ARG A 37 " pdb=" C ARG A 37 " pdb=" CB ARG A 37 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA PHE D 19 " pdb=" N PHE D 19 " pdb=" C PHE D 19 " pdb=" CB PHE D 19 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 965 not shown) Planarity restraints: 1144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS G 57 " -0.013 2.00e-02 2.50e+03 1.56e-02 3.63e+00 pdb=" CG HIS G 57 " 0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS G 57 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 HIS G 57 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS G 57 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS G 57 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 36 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" C ALA G 36 " -0.030 2.00e-02 2.50e+03 pdb=" O ALA G 36 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG G 37 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 20 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.67e+00 pdb=" C CYS A 20 " -0.028 2.00e-02 2.50e+03 pdb=" O CYS A 20 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN A 21 " 0.010 2.00e-02 2.50e+03 ... (remaining 1141 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 27 2.24 - 2.91: 2828 2.91 - 3.57: 10142 3.57 - 4.24: 15508 4.24 - 4.90: 26180 Nonbonded interactions: 54685 Sorted by model distance: nonbonded pdb=" NH2 ARG A 37 " pdb=" OE2 GLU B 26 " model vdw 1.578 2.520 nonbonded pdb=" OE1 GLN B 39 " pdb=" CZ2 TRP C 56 " model vdw 1.753 3.340 nonbonded pdb=" NH2 ARG B 43 " pdb=" CH2 TRP C 56 " model vdw 1.838 3.420 nonbonded pdb=" OE1 GLN C 39 " pdb=" CZ2 TRP G 56 " model vdw 1.889 3.340 nonbonded pdb=" NH2 ARG B 43 " pdb=" CZ3 TRP C 56 " model vdw 1.926 3.420 ... (remaining 54680 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.890 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 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 : 0.007 0.083 6496 Z= 0.452 Angle : 1.414 21.017 8840 Z= 0.997 Chirality : 0.058 0.343 968 Planarity : 0.005 0.036 1144 Dihedral : 15.900 84.850 2352 Min Nonbonded Distance : 1.578 Molprobity Statistics. All-atom Clashscore : 33.23 Ramachandran Plot: Outliers : 0.92 % Allowed : 4.08 % Favored : 95.00 % Rotamer: Outliers : 6.10 % Allowed : 9.16 % Favored : 84.74 % 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: -1.46 (0.26), residues: 760 helix: -0.53 (0.19), residues: 536 sheet: None (None), residues: 0 loop : -1.78 (0.33), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 56 HIS 0.019 0.003 HIS G 57 PHE 0.021 0.002 PHE I 72 TYR 0.026 0.003 TYR G 30 ARG 0.012 0.001 ARG L 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 516 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 3 residues processed: 524 average time/residue: 0.2245 time to fit residues: 145.4712 Evaluate side-chains 460 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 457 time to evaluate : 0.720 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3533 time to fit residues: 2.1810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 HIS A 63 GLN A 96 GLN B 60 ASN B 96 GLN ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN D 96 GLN E 18 ASN E 39 GLN E 60 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 ASN L 39 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN L 96 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.6489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 6496 Z= 0.309 Angle : 0.750 7.424 8840 Z= 0.390 Chirality : 0.043 0.144 968 Planarity : 0.007 0.048 1144 Dihedral : 4.870 21.411 880 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.11 % Favored : 97.63 % Rotamer: Outliers : 10.17 % Allowed : 27.03 % Favored : 62.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.27), residues: 760 helix: 1.14 (0.20), residues: 560 sheet: None (None), residues: 0 loop : -0.30 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP E 56 HIS 0.002 0.000 HIS I 57 PHE 0.033 0.003 PHE A 72 TYR 0.025 0.002 TYR L 92 ARG 0.008 0.001 ARG D 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 509 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 40 residues processed: 521 average time/residue: 0.2221 time to fit residues: 143.4522 Evaluate side-chains 518 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 478 time to evaluate : 0.743 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.0736 time to fit residues: 5.9050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 chunk 65 optimal weight: 0.6980 chunk 70 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 ASN ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 ASN C 63 GLN C 96 GLN D 39 GLN D 51 ASN D 63 GLN D 96 GLN E 60 ASN G 39 GLN G 60 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 ASN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.7923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6496 Z= 0.324 Angle : 0.721 9.075 8840 Z= 0.382 Chirality : 0.045 0.143 968 Planarity : 0.006 0.072 1144 Dihedral : 4.790 18.773 880 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.37 % Favored : 97.37 % Rotamer: Outliers : 7.85 % Allowed : 28.20 % Favored : 63.95 % 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: 1.39 (0.29), residues: 760 helix: 0.88 (0.20), residues: 600 sheet: None (None), residues: 0 loop : 1.62 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP L 56 HIS 0.002 0.001 HIS L 57 PHE 0.028 0.003 PHE G 72 TYR 0.022 0.002 TYR L 92 ARG 0.014 0.001 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 510 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 30 residues processed: 514 average time/residue: 0.2238 time to fit residues: 142.1876 Evaluate side-chains 505 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 475 time to evaluate : 0.811 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.0983 time to fit residues: 6.6079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN C 57 HIS C 96 GLN E 39 GLN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 ASN L 63 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.8516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6496 Z= 0.278 Angle : 0.754 11.413 8840 Z= 0.391 Chirality : 0.045 0.152 968 Planarity : 0.006 0.051 1144 Dihedral : 4.775 20.348 880 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.45 % Favored : 98.29 % Rotamer: Outliers : 5.38 % Allowed : 34.01 % Favored : 60.61 % 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: 0.86 (0.28), residues: 760 helix: 0.70 (0.20), residues: 552 sheet: None (None), residues: 0 loop : 0.59 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 56 HIS 0.003 0.001 HIS C 57 PHE 0.036 0.003 PHE D 72 TYR 0.026 0.002 TYR L 92 ARG 0.010 0.001 ARG D 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 490 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 20 residues processed: 499 average time/residue: 0.2400 time to fit residues: 149.0551 Evaluate side-chains 498 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 478 time to evaluate : 0.757 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0984 time to fit residues: 4.0110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 48 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 96 GLN ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 ASN ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 ASN I 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.8999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6496 Z= 0.258 Angle : 0.728 9.100 8840 Z= 0.387 Chirality : 0.045 0.158 968 Planarity : 0.006 0.065 1144 Dihedral : 4.725 25.330 880 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.11 % Favored : 97.63 % Rotamer: Outliers : 3.34 % Allowed : 40.12 % Favored : 56.54 % 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: 0.84 (0.29), residues: 760 helix: 0.36 (0.20), residues: 600 sheet: None (None), residues: 0 loop : 2.06 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 56 HIS 0.001 0.000 HIS A 57 PHE 0.030 0.002 PHE I 16 TYR 0.028 0.003 TYR L 9 ARG 0.010 0.001 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 495 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 496 average time/residue: 0.2239 time to fit residues: 137.4047 Evaluate side-chains 495 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 480 time to evaluate : 0.758 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0645 time to fit residues: 2.7648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 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 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.9399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6496 Z= 0.279 Angle : 0.768 9.657 8840 Z= 0.403 Chirality : 0.046 0.166 968 Planarity : 0.006 0.061 1144 Dihedral : 4.772 25.404 880 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 22.58 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.97 % Favored : 97.76 % Rotamer: Outliers : 3.34 % Allowed : 43.31 % Favored : 53.34 % 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: 0.64 (0.30), residues: 760 helix: 0.21 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 2.12 (0.55), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 56 HIS 0.001 0.000 HIS C 57 PHE 0.025 0.002 PHE D 16 TYR 0.028 0.003 TYR L 95 ARG 0.011 0.001 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 490 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 494 average time/residue: 0.2313 time to fit residues: 141.7918 Evaluate side-chains 493 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 478 time to evaluate : 0.680 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0646 time to fit residues: 2.7420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.9645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6496 Z= 0.272 Angle : 0.804 10.941 8840 Z= 0.419 Chirality : 0.046 0.167 968 Planarity : 0.006 0.053 1144 Dihedral : 4.825 26.855 880 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 25.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.24 % Favored : 97.50 % Rotamer: Outliers : 2.91 % Allowed : 45.20 % Favored : 51.89 % 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: 0.34 (0.29), residues: 760 helix: 0.22 (0.20), residues: 552 sheet: None (None), residues: 0 loop : 0.73 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 56 HIS 0.001 0.000 HIS A 57 PHE 0.029 0.002 PHE I 16 TYR 0.032 0.003 TYR I 9 ARG 0.011 0.002 ARG D 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 487 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 489 average time/residue: 0.2287 time to fit residues: 138.0269 Evaluate side-chains 486 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 476 time to evaluate : 0.714 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0643 time to fit residues: 2.1539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 66 optimal weight: 0.0000 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN D 39 GLN L 63 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.9893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6496 Z= 0.258 Angle : 0.841 14.153 8840 Z= 0.433 Chirality : 0.046 0.172 968 Planarity : 0.006 0.049 1144 Dihedral : 4.824 22.994 880 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 22.82 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.24 % Favored : 97.50 % Rotamer: Outliers : 2.91 % Allowed : 44.48 % Favored : 52.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.29), residues: 760 helix: 0.12 (0.20), residues: 552 sheet: None (None), residues: 0 loop : 0.60 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 56 HIS 0.001 0.000 HIS E 57 PHE 0.026 0.002 PHE D 16 TYR 0.043 0.003 TYR I 9 ARG 0.011 0.001 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 491 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 493 average time/residue: 0.2346 time to fit residues: 142.4270 Evaluate side-chains 484 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 474 time to evaluate : 0.744 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0636 time to fit residues: 2.1793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 64 optimal weight: 0.0970 chunk 42 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 51 ASN E 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 1.0142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6496 Z= 0.277 Angle : 0.901 16.510 8840 Z= 0.459 Chirality : 0.047 0.203 968 Planarity : 0.006 0.058 1144 Dihedral : 4.939 21.554 880 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 23.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.63 % Favored : 97.11 % Rotamer: Outliers : 1.74 % Allowed : 46.51 % Favored : 51.74 % 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: 0.03 (0.29), residues: 760 helix: 0.02 (0.20), residues: 560 sheet: None (None), residues: 0 loop : 0.54 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 56 HIS 0.001 0.000 HIS E 57 PHE 0.022 0.002 PHE I 16 TYR 0.040 0.003 TYR I 9 ARG 0.014 0.002 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 482 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 485 average time/residue: 0.2269 time to fit residues: 137.0898 Evaluate side-chains 481 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 475 time to evaluate : 0.689 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0647 time to fit residues: 1.6651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 44 optimal weight: 0.0670 chunk 35 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 ASN D 96 GLN E 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 1.0280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6496 Z= 0.270 Angle : 0.951 16.187 8840 Z= 0.479 Chirality : 0.047 0.194 968 Planarity : 0.006 0.050 1144 Dihedral : 5.073 21.550 880 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.50 % Favored : 97.24 % Rotamer: Outliers : 0.73 % Allowed : 48.55 % Favored : 50.73 % 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: -0.07 (0.29), residues: 760 helix: -0.06 (0.20), residues: 560 sheet: None (None), residues: 0 loop : 0.51 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 56 HIS 0.002 0.000 HIS I 57 PHE 0.027 0.003 PHE E 3 TYR 0.049 0.003 TYR C 9 ARG 0.016 0.002 ARG A 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 491 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 491 average time/residue: 0.2369 time to fit residues: 142.3485 Evaluate side-chains 487 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 482 time to evaluate : 0.761 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0669 time to fit residues: 1.6258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.073786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.064438 restraints weight = 22305.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.066628 restraints weight = 11978.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.068150 restraints weight = 7619.107| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 1.0399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6496 Z= 0.312 Angle : 0.983 17.286 8840 Z= 0.499 Chirality : 0.050 0.198 968 Planarity : 0.007 0.087 1144 Dihedral : 5.111 20.934 880 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 25.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.63 % Favored : 97.11 % Rotamer: Outliers : 1.60 % Allowed : 48.84 % Favored : 49.56 % 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: -0.15 (0.29), residues: 760 helix: -0.10 (0.20), residues: 560 sheet: None (None), residues: 0 loop : 0.44 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.003 TRP E 56 HIS 0.001 0.000 HIS B 57 PHE 0.043 0.003 PHE I 59 TYR 0.036 0.003 TYR E 9 ARG 0.015 0.002 ARG A 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2380.15 seconds wall clock time: 43 minutes 20.70 seconds (2600.70 seconds total)