Starting phenix.real_space_refine on Mon Sep 23 12:17:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az4_15753/09_2024/8az4_15753.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az4_15753/09_2024/8az4_15753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az4_15753/09_2024/8az4_15753.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az4_15753/09_2024/8az4_15753.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az4_15753/09_2024/8az4_15753.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az4_15753/09_2024/8az4_15753.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 1350 2.51 5 N 420 2.21 5 O 510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 2280 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "G" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "H" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "J" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Time building chain proxies: 3.40, per 1000 atoms: 1.49 Number of scatterers: 2280 At special positions: 0 Unit cell: (69.3, 72.9, 45, 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 510 8.00 N 420 7.00 C 1350 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 534.0 milliseconds 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 520 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 53.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 22 removed outlier: 6.979A pdb=" N ASN A 21 " --> pdb=" O GLY C 20 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASN C 22 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ASN C 21 " --> pdb=" O GLY E 20 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN E 22 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN E 21 " --> pdb=" O GLY G 20 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN G 22 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASN G 21 " --> pdb=" O GLY I 20 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASN I 22 " --> pdb=" O ASN G 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 32 Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 22 removed outlier: 6.937A pdb=" N ASN B 21 " --> pdb=" O GLY D 20 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ASN D 22 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASN D 21 " --> pdb=" O GLY F 20 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASN F 22 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ASN F 21 " --> pdb=" O GLY H 20 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASN H 22 " --> pdb=" O ASN F 21 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN H 21 " --> pdb=" O GLY J 20 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN J 22 " --> pdb=" O ASN H 21 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.599A pdb=" N SER B 29 " --> pdb=" O THR D 30 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N VAL D 32 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASN B 31 " --> pdb=" O VAL D 32 " (cutoff:3.500A) 101 hydrogen bonds defined for protein. 295 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.58 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 340 1.28 - 1.35: 400 1.35 - 1.41: 290 1.41 - 1.48: 320 1.48 - 1.54: 870 Bond restraints: 2220 Sorted by residual: bond pdb=" CG ASN E 35 " pdb=" ND2 ASN E 35 " ideal model delta sigma weight residual 1.328 1.312 0.016 2.10e-02 2.27e+03 6.10e-01 bond pdb=" CB ASN D 31 " pdb=" CG ASN D 31 " ideal model delta sigma weight residual 1.516 1.497 0.019 2.50e-02 1.60e+03 6.06e-01 bond pdb=" CD2 TYR C 37 " pdb=" CE2 TYR C 37 " ideal model delta sigma weight residual 1.382 1.359 0.023 3.00e-02 1.11e+03 5.75e-01 bond pdb=" CG1 ILE I 26 " pdb=" CD1 ILE I 26 " ideal model delta sigma weight residual 1.513 1.484 0.029 3.90e-02 6.57e+02 5.65e-01 bond pdb=" CG ASN F 31 " pdb=" OD1 ASN F 31 " ideal model delta sigma weight residual 1.231 1.217 0.014 1.90e-02 2.77e+03 5.56e-01 ... (remaining 2215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 2571 0.95 - 1.90: 373 1.90 - 2.85: 59 2.85 - 3.80: 12 3.80 - 4.75: 5 Bond angle restraints: 3020 Sorted by residual: angle pdb=" N THR C 30 " pdb=" CA THR C 30 " pdb=" C THR C 30 " ideal model delta sigma weight residual 109.40 112.94 -3.54 1.63e+00 3.76e-01 4.71e+00 angle pdb=" N THR I 30 " pdb=" CA THR I 30 " pdb=" C THR I 30 " ideal model delta sigma weight residual 109.24 112.77 -3.53 1.67e+00 3.59e-01 4.46e+00 angle pdb=" N THR G 30 " pdb=" CA THR G 30 " pdb=" C THR G 30 " ideal model delta sigma weight residual 109.40 112.77 -3.37 1.63e+00 3.76e-01 4.27e+00 angle pdb=" N THR A 30 " pdb=" CA THR A 30 " pdb=" C THR A 30 " ideal model delta sigma weight residual 109.40 112.76 -3.36 1.63e+00 3.76e-01 4.26e+00 angle pdb=" N SER F 34 " pdb=" CA SER F 34 " pdb=" C SER F 34 " ideal model delta sigma weight residual 111.54 114.31 -2.77 1.36e+00 5.41e-01 4.14e+00 ... (remaining 3015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.77: 1130 10.77 - 21.54: 86 21.54 - 32.31: 29 32.31 - 43.08: 10 43.08 - 53.85: 5 Dihedral angle restraints: 1260 sinusoidal: 440 harmonic: 820 Sorted by residual: dihedral pdb=" CA LEU I 27 " pdb=" CB LEU I 27 " pdb=" CG LEU I 27 " pdb=" CD1 LEU I 27 " ideal model delta sinusoidal sigma weight residual 180.00 146.98 33.02 3 1.50e+01 4.44e-03 5.49e+00 dihedral pdb=" CA LEU E 27 " pdb=" CB LEU E 27 " pdb=" CG LEU E 27 " pdb=" CD1 LEU E 27 " ideal model delta sinusoidal sigma weight residual 180.00 147.02 32.98 3 1.50e+01 4.44e-03 5.48e+00 dihedral pdb=" CA LEU G 27 " pdb=" CB LEU G 27 " pdb=" CG LEU G 27 " pdb=" CD1 LEU G 27 " ideal model delta sinusoidal sigma weight residual 180.00 147.07 32.93 3 1.50e+01 4.44e-03 5.46e+00 ... (remaining 1257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 162 0.031 - 0.062: 114 0.062 - 0.093: 21 0.093 - 0.124: 31 0.124 - 0.155: 12 Chirality restraints: 340 Sorted by residual: chirality pdb=" CA ILE G 26 " pdb=" N ILE G 26 " pdb=" C ILE G 26 " pdb=" CB ILE G 26 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.02e-01 chirality pdb=" CA ILE A 26 " pdb=" N ILE A 26 " pdb=" C ILE A 26 " pdb=" CB ILE A 26 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA ILE H 26 " pdb=" N ILE H 26 " pdb=" C ILE H 26 " pdb=" CB ILE H 26 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.54e-01 ... (remaining 337 not shown) Planarity restraints: 400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU G 27 " -0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" C LEU G 27 " 0.020 2.00e-02 2.50e+03 pdb=" O LEU G 27 " -0.008 2.00e-02 2.50e+03 pdb=" N SER G 28 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 29 " -0.005 2.00e-02 2.50e+03 1.08e-02 1.16e+00 pdb=" C SER C 29 " 0.019 2.00e-02 2.50e+03 pdb=" O SER C 29 " -0.007 2.00e-02 2.50e+03 pdb=" N THR C 30 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 27 " -0.005 2.00e-02 2.50e+03 1.06e-02 1.12e+00 pdb=" C LEU E 27 " 0.018 2.00e-02 2.50e+03 pdb=" O LEU E 27 " -0.007 2.00e-02 2.50e+03 pdb=" N SER E 28 " -0.006 2.00e-02 2.50e+03 ... (remaining 397 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 525 2.81 - 3.34: 1772 3.34 - 3.86: 4197 3.86 - 4.38: 4580 4.38 - 4.90: 8397 Nonbonded interactions: 19471 Sorted by model distance: nonbonded pdb=" OH TYR D 37 " pdb=" O HOH D 101 " model vdw 2.292 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O HOH C 101 " model vdw 2.295 3.040 nonbonded pdb=" OH TYR E 37 " pdb=" O HOH E 101 " model vdw 2.316 3.040 nonbonded pdb=" OH TYR J 37 " pdb=" O HOH J 101 " model vdw 2.322 3.040 nonbonded pdb=" OG SER J 19 " pdb=" O HOH J 102 " model vdw 2.335 3.040 ... (remaining 19466 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 17 or resid 19 through 37 or resid 38)) selection = (chain 'B' and (resid 10 through 17 or resid 19 through 37 or resid 38)) selection = (chain 'C' and (resid 10 through 17 or resid 19 through 37 or resid 38)) selection = (chain 'D' and (resid 10 through 17 or resid 19 through 37 or resid 38)) selection = (chain 'E' and (resid 10 through 17 or resid 19 through 37 or resid 38)) selection = (chain 'F' and (resid 10 through 17 or resid 19 through 37 or resid 38)) selection = (chain 'G' and (resid 10 through 17 or resid 19 through 37 or resid 38)) selection = (chain 'H' and (resid 10 through 17 or resid 19 through 37 or resid 38)) selection = (chain 'I' and (resid 10 through 17 or resid 19 through 37 or resid 38)) selection = (chain 'J' and (resid 10 through 17 or resid 19 through 37 or resid 38)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.97 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 12.640 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 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 : 0.006 0.029 2220 Z= 0.418 Angle : 0.720 4.752 3020 Z= 0.431 Chirality : 0.053 0.155 340 Planarity : 0.003 0.012 400 Dihedral : 10.223 53.851 740 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.28), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.21), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE E 15 TYR 0.010 0.002 TYR E 37 ARG 0.002 0.001 ARG J 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.235 Fit side-chains REVERT: B 11 ARG cc_start: 0.7613 (mtt180) cc_final: 0.7266 (mmt180) REVERT: I 11 ARG cc_start: 0.7796 (mtt180) cc_final: 0.7553 (mtt-85) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 1.3220 time to fit residues: 44.6642 Evaluate side-chains 32 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A A 21 ASN B 21 ASN C 18 HIS A C 21 ASN D 18 HIS A D 21 ASN E 18 HIS A E 21 ASN F 18 HIS A F 21 ASN G 18 HIS A G 21 ASN H 21 ASN I 18 HIS A I 21 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2220 Z= 0.228 Angle : 0.662 5.880 3020 Z= 0.348 Chirality : 0.049 0.137 340 Planarity : 0.002 0.012 400 Dihedral : 4.272 10.504 310 Min Nonbonded Distance : 2.673 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.42 % Allowed : 10.83 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.31), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.24), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE H 15 TYR 0.003 0.001 TYR A 37 ARG 0.003 0.000 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7277 (mmm-85) REVERT: J 11 ARG cc_start: 0.7948 (mmm-85) cc_final: 0.7334 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 1.1023 time to fit residues: 37.3715 Evaluate side-chains 32 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.020 2220 Z= 0.309 Angle : 0.720 6.182 3020 Z= 0.378 Chirality : 0.050 0.137 340 Planarity : 0.003 0.009 400 Dihedral : 4.262 10.533 310 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.67 % Allowed : 10.42 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.29), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.22), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE E 15 TYR 0.006 0.001 TYR C 37 ARG 0.002 0.000 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7455 (mmm-85) REVERT: J 11 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7530 (mmm-85) outliers start: 4 outliers final: 0 residues processed: 29 average time/residue: 1.3648 time to fit residues: 40.5628 Evaluate side-chains 31 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain J residue 11 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 5 optimal weight: 0.5980 chunk 16 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 2220 Z= 0.208 Angle : 0.630 6.373 3020 Z= 0.325 Chirality : 0.047 0.133 340 Planarity : 0.002 0.008 400 Dihedral : 4.169 10.055 310 Min Nonbonded Distance : 2.680 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.08 % Allowed : 10.00 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.29), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.22), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE C 15 TYR 0.005 0.001 TYR C 37 ARG 0.002 0.000 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7461 (mmm-85) REVERT: G 11 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.7069 (mtm-85) REVERT: H 16 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8217 (tt) REVERT: J 11 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7379 (mtm-85) outliers start: 5 outliers final: 1 residues processed: 29 average time/residue: 1.3397 time to fit residues: 39.8193 Evaluate side-chains 33 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 29 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.021 2220 Z= 0.325 Angle : 0.710 6.400 3020 Z= 0.375 Chirality : 0.049 0.135 340 Planarity : 0.003 0.007 400 Dihedral : 4.240 10.063 310 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.08 % Allowed : 10.00 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.29), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.22), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE E 15 TYR 0.007 0.001 TYR C 37 ARG 0.002 0.000 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7523 (mmm-85) REVERT: H 16 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8271 (tt) REVERT: J 11 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7585 (mmm-85) outliers start: 5 outliers final: 1 residues processed: 31 average time/residue: 1.3568 time to fit residues: 43.0347 Evaluate side-chains 34 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 29 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 2220 Z= 0.123 Angle : 0.551 7.085 3020 Z= 0.277 Chirality : 0.045 0.133 340 Planarity : 0.001 0.006 400 Dihedral : 4.025 9.480 310 Min Nonbonded Distance : 2.699 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.67 % Allowed : 10.42 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.30), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.23), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE D 15 TYR 0.003 0.001 TYR I 37 ARG 0.002 0.000 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.306 Fit side-chains REVERT: G 11 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7044 (mtm-85) REVERT: H 16 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8199 (tt) REVERT: J 11 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7400 (mtm-85) outliers start: 4 outliers final: 0 residues processed: 28 average time/residue: 1.2932 time to fit residues: 37.1214 Evaluate side-chains 31 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain J residue 11 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 17 optimal weight: 0.0170 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 overall best weight: 1.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2220 Z= 0.180 Angle : 0.601 7.272 3020 Z= 0.305 Chirality : 0.045 0.132 340 Planarity : 0.002 0.005 400 Dihedral : 4.080 9.469 310 Min Nonbonded Distance : 2.694 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.25 % Allowed : 11.25 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.30), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.23), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE D 15 TYR 0.004 0.001 TYR C 37 ARG 0.001 0.000 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: H 16 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8233 (tt) REVERT: J 11 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7404 (mtm-85) outliers start: 3 outliers final: 1 residues processed: 29 average time/residue: 1.2716 time to fit residues: 37.8142 Evaluate side-chains 31 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 29 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 17 optimal weight: 0.0770 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 overall best weight: 1.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 2220 Z= 0.183 Angle : 0.609 7.021 3020 Z= 0.309 Chirality : 0.045 0.131 340 Planarity : 0.002 0.005 400 Dihedral : 4.080 9.517 310 Min Nonbonded Distance : 2.694 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.50 % Allowed : 9.58 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.30), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.23), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE C 15 TYR 0.004 0.001 TYR C 37 ARG 0.001 0.000 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 28 time to evaluate : 0.250 Fit side-chains REVERT: A 11 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7313 (mmm-85) REVERT: D 11 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7123 (mmm-85) REVERT: G 11 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7070 (mtm-85) REVERT: H 16 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8289 (tt) REVERT: J 11 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7401 (mtm-85) outliers start: 6 outliers final: 1 residues processed: 30 average time/residue: 1.3111 time to fit residues: 40.2519 Evaluate side-chains 34 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 28 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 29 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2220 Z= 0.167 Angle : 0.609 7.266 3020 Z= 0.302 Chirality : 0.045 0.131 340 Planarity : 0.002 0.005 400 Dihedral : 4.063 9.520 310 Min Nonbonded Distance : 2.698 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.08 % Allowed : 10.83 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.30), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.23), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE C 15 TYR 0.004 0.001 TYR C 37 ARG 0.001 0.000 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 0.255 Fit side-chains REVERT: A 11 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7305 (mmm-85) REVERT: G 11 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.7067 (mtm-85) REVERT: H 16 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8239 (tt) REVERT: J 11 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7402 (mtm-85) outliers start: 5 outliers final: 1 residues processed: 29 average time/residue: 1.2918 time to fit residues: 38.4210 Evaluate side-chains 33 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 29 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.020 2220 Z= 0.308 Angle : 0.706 6.708 3020 Z= 0.367 Chirality : 0.048 0.134 340 Planarity : 0.002 0.007 400 Dihedral : 4.182 9.871 310 Min Nonbonded Distance : 2.663 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.08 % Allowed : 10.42 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.30), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.23), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE H 15 TYR 0.007 0.001 TYR C 37 ARG 0.001 0.000 ARG I 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 29 time to evaluate : 0.253 Fit side-chains REVERT: G 11 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7080 (mtm-85) REVERT: H 16 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8315 (tt) REVERT: J 11 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7614 (mmm-85) outliers start: 5 outliers final: 1 residues processed: 30 average time/residue: 1.2533 time to fit residues: 38.5627 Evaluate side-chains 33 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 29 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.098294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.071433 restraints weight = 16562.795| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.01 r_work: 0.3054 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2220 Z= 0.286 Angle : 0.704 7.084 3020 Z= 0.361 Chirality : 0.048 0.134 340 Planarity : 0.002 0.007 400 Dihedral : 4.174 9.882 310 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.67 % Allowed : 11.25 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.29), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.22), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE H 15 TYR 0.006 0.001 TYR C 37 ARG 0.002 0.000 ARG A 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1346.46 seconds wall clock time: 24 minutes 38.07 seconds (1478.07 seconds total)