Starting phenix.real_space_refine on Fri Sep 27 02:44:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl1_16709/09_2024/8cl1_16709.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl1_16709/09_2024/8cl1_16709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl1_16709/09_2024/8cl1_16709.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl1_16709/09_2024/8cl1_16709.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl1_16709/09_2024/8cl1_16709.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl1_16709/09_2024/8cl1_16709.cif" } resolution = 3.35 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= 0.002 sd= 0.067 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 5472 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 72 5.16 5 C 6660 2.51 5 N 1818 2.21 5 O 1944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10494 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1646 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 103 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, E, G, I, K, D, F, H, J, L Time building chain proxies: 4.48, per 1000 atoms: 0.43 Number of scatterers: 10494 At special positions: 0 Unit cell: (116.25, 108.81, 70.68, 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 72 16.00 O 1944 8.00 N 1818 7.00 C 6660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.3 seconds 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 6 sheets defined 69.2% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 119 Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 175 removed outlier: 3.723A pdb=" N ALA A 174 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.505A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.651A pdb=" N GLY A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'C' and resid 16 through 31 Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 175 removed outlier: 3.723A pdb=" N ALA C 174 " --> pdb=" O LYS C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 193 removed outlier: 4.505A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.651A pdb=" N GLY C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 219 Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 58 Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 110 through 119 Processing helix chain 'E' and resid 125 through 146 Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 160 through 175 removed outlier: 3.723A pdb=" N ALA E 174 " --> pdb=" O LYS E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 193 removed outlier: 4.505A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.650A pdb=" N GLY E 206 " --> pdb=" O LEU E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 219 Processing helix chain 'G' and resid 16 through 31 Processing helix chain 'G' and resid 35 through 44 Processing helix chain 'G' and resid 48 through 58 Processing helix chain 'G' and resid 62 through 84 Processing helix chain 'G' and resid 100 through 105 Processing helix chain 'G' and resid 110 through 119 Processing helix chain 'G' and resid 125 through 146 Processing helix chain 'G' and resid 149 through 153 Processing helix chain 'G' and resid 160 through 175 removed outlier: 3.723A pdb=" N ALA G 174 " --> pdb=" O LYS G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 193 removed outlier: 4.505A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 removed outlier: 3.651A pdb=" N GLY G 206 " --> pdb=" O LEU G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 219 Processing helix chain 'I' and resid 16 through 31 Processing helix chain 'I' and resid 35 through 44 Processing helix chain 'I' and resid 48 through 58 Processing helix chain 'I' and resid 62 through 84 Processing helix chain 'I' and resid 100 through 105 Processing helix chain 'I' and resid 110 through 119 Processing helix chain 'I' and resid 125 through 146 Processing helix chain 'I' and resid 149 through 153 Processing helix chain 'I' and resid 160 through 175 removed outlier: 3.723A pdb=" N ALA I 174 " --> pdb=" O LYS I 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 193 removed outlier: 4.505A pdb=" N LEU I 190 " --> pdb=" O THR I 186 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL I 191 " --> pdb=" O GLU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 206 removed outlier: 3.651A pdb=" N GLY I 206 " --> pdb=" O LEU I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 219 Processing helix chain 'K' and resid 16 through 31 Processing helix chain 'K' and resid 35 through 44 Processing helix chain 'K' and resid 48 through 58 Processing helix chain 'K' and resid 62 through 84 Processing helix chain 'K' and resid 100 through 105 Processing helix chain 'K' and resid 110 through 119 Processing helix chain 'K' and resid 125 through 146 Processing helix chain 'K' and resid 149 through 153 Processing helix chain 'K' and resid 160 through 175 removed outlier: 3.723A pdb=" N ALA K 174 " --> pdb=" O LYS K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 193 removed outlier: 4.505A pdb=" N LEU K 190 " --> pdb=" O THR K 186 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL K 191 " --> pdb=" O GLU K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 206 removed outlier: 3.650A pdb=" N GLY K 206 " --> pdb=" O LEU K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 219 Processing sheet with id=1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=2, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=3, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=4, first strand: chain 'G' and resid 2 through 4 Processing sheet with id=5, first strand: chain 'I' and resid 2 through 4 Processing sheet with id=6, first strand: chain 'K' and resid 2 through 4 648 hydrogen bonds defined for protein. 1908 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: 2.66 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1776 1.29 - 1.42: 2508 1.42 - 1.55: 6312 1.55 - 1.68: 18 1.68 - 1.81: 132 Bond restraints: 10746 Sorted by residual: bond pdb=" CA ALA I 177 " pdb=" C ALA I 177 " ideal model delta sigma weight residual 1.525 1.428 0.097 1.28e-02 6.10e+03 5.74e+01 bond pdb=" CA ALA C 177 " pdb=" C ALA C 177 " ideal model delta sigma weight residual 1.525 1.428 0.097 1.28e-02 6.10e+03 5.74e+01 bond pdb=" CA ALA G 177 " pdb=" C ALA G 177 " ideal model delta sigma weight residual 1.525 1.428 0.097 1.28e-02 6.10e+03 5.72e+01 bond pdb=" CA ALA A 177 " pdb=" C ALA A 177 " ideal model delta sigma weight residual 1.525 1.428 0.097 1.28e-02 6.10e+03 5.72e+01 bond pdb=" CA ALA E 177 " pdb=" C ALA E 177 " ideal model delta sigma weight residual 1.525 1.428 0.097 1.28e-02 6.10e+03 5.68e+01 ... (remaining 10741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 13266 1.39 - 2.78: 1026 2.78 - 4.17: 276 4.17 - 5.56: 36 5.56 - 6.95: 18 Bond angle restraints: 14622 Sorted by residual: angle pdb=" N ALA C 177 " pdb=" CA ALA C 177 " pdb=" C ALA C 177 " ideal model delta sigma weight residual 110.35 117.30 -6.95 1.36e+00 5.41e-01 2.61e+01 angle pdb=" N ALA I 177 " pdb=" CA ALA I 177 " pdb=" C ALA I 177 " ideal model delta sigma weight residual 110.35 117.30 -6.95 1.36e+00 5.41e-01 2.61e+01 angle pdb=" N ALA K 177 " pdb=" CA ALA K 177 " pdb=" C ALA K 177 " ideal model delta sigma weight residual 110.35 117.29 -6.94 1.36e+00 5.41e-01 2.60e+01 angle pdb=" N ALA E 177 " pdb=" CA ALA E 177 " pdb=" C ALA E 177 " ideal model delta sigma weight residual 110.35 117.29 -6.94 1.36e+00 5.41e-01 2.60e+01 angle pdb=" N ALA G 177 " pdb=" CA ALA G 177 " pdb=" C ALA G 177 " ideal model delta sigma weight residual 110.35 117.25 -6.90 1.36e+00 5.41e-01 2.57e+01 ... (remaining 14617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 6012 15.12 - 30.23: 396 30.23 - 45.35: 96 45.35 - 60.46: 30 60.46 - 75.58: 12 Dihedral angle restraints: 6546 sinusoidal: 2634 harmonic: 3912 Sorted by residual: dihedral pdb=" CA PHE C 32 " pdb=" C PHE C 32 " pdb=" N SER C 33 " pdb=" CA SER C 33 " ideal model delta harmonic sigma weight residual 180.00 149.91 30.09 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" CA PHE I 32 " pdb=" C PHE I 32 " pdb=" N SER I 33 " pdb=" CA SER I 33 " ideal model delta harmonic sigma weight residual 180.00 149.91 30.09 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" CA PHE K 32 " pdb=" C PHE K 32 " pdb=" N SER K 33 " pdb=" CA SER K 33 " ideal model delta harmonic sigma weight residual 180.00 149.92 30.08 0 5.00e+00 4.00e-02 3.62e+01 ... (remaining 6543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1452 0.084 - 0.167: 162 0.167 - 0.250: 18 0.250 - 0.334: 0 0.334 - 0.417: 6 Chirality restraints: 1638 Sorted by residual: chirality pdb=" CA ALA C 177 " pdb=" N ALA C 177 " pdb=" C ALA C 177 " pdb=" CB ALA C 177 " both_signs ideal model delta sigma weight residual False 2.48 2.07 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CA ALA I 177 " pdb=" N ALA I 177 " pdb=" C ALA I 177 " pdb=" CB ALA I 177 " both_signs ideal model delta sigma weight residual False 2.48 2.07 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CA ALA K 177 " pdb=" N ALA K 177 " pdb=" C ALA K 177 " pdb=" CB ALA K 177 " both_signs ideal model delta sigma weight residual False 2.48 2.07 0.41 2.00e-01 2.50e+01 4.30e+00 ... (remaining 1635 not shown) Planarity restraints: 1902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU I 175 " 0.015 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C GLU I 175 " -0.050 2.00e-02 2.50e+03 pdb=" O GLU I 175 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN I 176 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 175 " 0.015 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C GLU A 175 " -0.050 2.00e-02 2.50e+03 pdb=" O GLU A 175 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN A 176 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 175 " -0.015 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C GLU G 175 " 0.050 2.00e-02 2.50e+03 pdb=" O GLU G 175 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN G 176 " -0.017 2.00e-02 2.50e+03 ... (remaining 1899 not shown) Histogram of nonbonded interaction distances: 0.39 - 1.29: 24 1.29 - 2.20: 78 2.20 - 3.10: 8266 3.10 - 4.00: 27982 4.00 - 4.90: 51004 Warning: very small nonbonded interaction distances. Nonbonded interactions: 87354 Sorted by model distance: nonbonded pdb=" CZ TYR G 145 " pdb=" NH2 ARG I 162 " model vdw 0.393 3.340 nonbonded pdb=" CZ TYR A 145 " pdb=" NH2 ARG C 162 " model vdw 0.393 3.340 nonbonded pdb=" CZ TYR C 145 " pdb=" NH2 ARG E 162 " model vdw 0.393 3.340 nonbonded pdb=" CZ TYR I 145 " pdb=" NH2 ARG K 162 " model vdw 0.393 3.340 nonbonded pdb=" NH2 ARG A 162 " pdb=" CZ TYR K 145 " model vdw 0.393 3.340 ... (remaining 87349 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' 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 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: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 24.450 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 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 : 0.008 0.097 10746 Z= 0.536 Angle : 0.929 6.951 14622 Z= 0.576 Chirality : 0.059 0.417 1638 Planarity : 0.008 0.055 1902 Dihedral : 12.178 75.578 4002 Min Nonbonded Distance : 0.393 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.90 % Allowed : 0.00 % Favored : 99.10 % Rotamer: Outliers : 0.54 % Allowed : 0.00 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -1.05 (0.20), residues: 1326 helix: -0.93 (0.14), residues: 870 sheet: -3.06 (0.31), residues: 54 loop : 0.80 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP E 23 HIS 0.008 0.002 HIS C 84 PHE 0.014 0.003 PHE B 321 TYR 0.026 0.006 TYR C 145 ARG 0.015 0.002 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 226 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.7951 (tpt) cc_final: 0.7734 (tpp) REVERT: A 75 GLU cc_start: 0.7905 (pt0) cc_final: 0.7666 (pt0) REVERT: C 39 MET cc_start: 0.7700 (tpt) cc_final: 0.7151 (tpp) REVERT: G 39 MET cc_start: 0.7952 (tpt) cc_final: 0.7732 (tpp) REVERT: G 75 GLU cc_start: 0.7907 (pt0) cc_final: 0.7669 (pt0) REVERT: I 39 MET cc_start: 0.7691 (tpt) cc_final: 0.7151 (tpp) outliers start: 6 outliers final: 2 residues processed: 226 average time/residue: 0.2681 time to fit residues: 80.9182 Evaluate side-chains 142 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain G residue 176 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 119 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN C 74 ASN E 74 ASN G 74 ASN I 74 ASN K 74 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10746 Z= 0.238 Angle : 0.641 7.397 14622 Z= 0.336 Chirality : 0.043 0.151 1638 Planarity : 0.006 0.041 1902 Dihedral : 5.344 50.065 1434 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.90 % Allowed : 0.45 % Favored : 98.64 % Rotamer: Outliers : 0.72 % Allowed : 4.12 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.10 (0.22), residues: 1326 helix: 0.99 (0.17), residues: 876 sheet: -1.87 (0.34), residues: 54 loop : 0.87 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 117 HIS 0.002 0.001 HIS I 84 PHE 0.007 0.001 PHE J 321 TYR 0.011 0.001 TYR C 169 ARG 0.005 0.001 ARG I 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 180 time to evaluate : 1.139 Fit side-chains REVERT: A 145 TYR cc_start: 0.7106 (m-80) cc_final: 0.6339 (m-10) REVERT: A 176 GLN cc_start: 0.6488 (OUTLIER) cc_final: 0.6224 (pt0) REVERT: C 25 LYS cc_start: 0.8560 (mttt) cc_final: 0.8295 (mttt) REVERT: C 39 MET cc_start: 0.7503 (tpt) cc_final: 0.6757 (tpp) REVERT: C 145 TYR cc_start: 0.7296 (m-80) cc_final: 0.6543 (m-10) REVERT: E 145 TYR cc_start: 0.7178 (m-80) cc_final: 0.6348 (m-10) REVERT: G 145 TYR cc_start: 0.7105 (m-80) cc_final: 0.6338 (m-10) REVERT: G 176 GLN cc_start: 0.6485 (OUTLIER) cc_final: 0.6223 (pt0) REVERT: I 25 LYS cc_start: 0.8561 (mttt) cc_final: 0.8293 (mttt) REVERT: I 39 MET cc_start: 0.7504 (tpt) cc_final: 0.6757 (tpp) REVERT: I 145 TYR cc_start: 0.7296 (m-80) cc_final: 0.6545 (m-10) REVERT: K 145 TYR cc_start: 0.7178 (m-80) cc_final: 0.6351 (m-10) outliers start: 8 outliers final: 0 residues processed: 184 average time/residue: 0.2571 time to fit residues: 63.8627 Evaluate side-chains 170 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain G residue 176 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN G 176 GLN G 179 GLN K 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10746 Z= 0.341 Angle : 0.637 6.906 14622 Z= 0.331 Chirality : 0.043 0.167 1638 Planarity : 0.006 0.047 1902 Dihedral : 5.071 48.245 1434 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.81 % Favored : 97.74 % Rotamer: Outliers : 1.25 % Allowed : 5.91 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.35 (0.23), residues: 1326 helix: 1.10 (0.17), residues: 870 sheet: -1.45 (0.39), residues: 54 loop : 1.12 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 117 HIS 0.004 0.001 HIS K 12 PHE 0.005 0.001 PHE G 161 TYR 0.008 0.001 TYR I 169 ARG 0.005 0.001 ARG I 162 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 173 time to evaluate : 1.237 Fit side-chains REVERT: A 25 LYS cc_start: 0.8581 (mttt) cc_final: 0.8093 (mttm) REVERT: A 104 ILE cc_start: 0.8168 (mt) cc_final: 0.7865 (mm) REVERT: E 25 LYS cc_start: 0.8612 (mttt) cc_final: 0.8185 (mttm) REVERT: G 25 LYS cc_start: 0.8586 (mttt) cc_final: 0.8094 (mttm) REVERT: G 104 ILE cc_start: 0.8165 (mt) cc_final: 0.7869 (mm) REVERT: K 25 LYS cc_start: 0.8610 (mttt) cc_final: 0.8185 (mttm) outliers start: 14 outliers final: 10 residues processed: 179 average time/residue: 0.2502 time to fit residues: 61.3167 Evaluate side-chains 177 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 167 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain I residue 176 GLN Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 127 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN C 179 GLN ** I 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10746 Z= 0.278 Angle : 0.588 7.040 14622 Z= 0.303 Chirality : 0.041 0.157 1638 Planarity : 0.006 0.048 1902 Dihedral : 4.840 48.374 1434 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.66 % Favored : 97.89 % Rotamer: Outliers : 1.25 % Allowed : 7.17 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.45 (0.23), residues: 1326 helix: 1.14 (0.17), residues: 870 sheet: -0.97 (0.48), residues: 54 loop : 1.21 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 117 HIS 0.003 0.001 HIS G 12 PHE 0.006 0.001 PHE G 32 TYR 0.008 0.001 TYR I 169 ARG 0.004 0.001 ARG I 162 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 183 time to evaluate : 1.090 Fit side-chains REVERT: A 39 MET cc_start: 0.7410 (tpp) cc_final: 0.6804 (tpp) REVERT: A 113 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6311 (tt0) REVERT: C 15 ILE cc_start: 0.8116 (mt) cc_final: 0.7876 (mm) REVERT: C 117 TRP cc_start: 0.6205 (m-10) cc_final: 0.5962 (m-10) REVERT: C 144 MET cc_start: 0.8080 (tpp) cc_final: 0.7762 (tpp) REVERT: G 39 MET cc_start: 0.7415 (tpp) cc_final: 0.6805 (tpp) REVERT: G 113 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6308 (tt0) REVERT: I 15 ILE cc_start: 0.8119 (mt) cc_final: 0.7879 (mm) REVERT: I 117 TRP cc_start: 0.6202 (m-10) cc_final: 0.5954 (m-10) REVERT: I 144 MET cc_start: 0.8080 (tpp) cc_final: 0.7765 (tpp) outliers start: 14 outliers final: 10 residues processed: 189 average time/residue: 0.2400 time to fit residues: 62.2401 Evaluate side-chains 171 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 161 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain I residue 176 GLN Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 95 optimal weight: 0.9980 chunk 52 optimal weight: 0.0980 chunk 108 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10746 Z= 0.205 Angle : 0.554 7.042 14622 Z= 0.285 Chirality : 0.040 0.147 1638 Planarity : 0.005 0.051 1902 Dihedral : 4.703 48.963 1434 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.81 % Favored : 97.74 % Rotamer: Outliers : 1.25 % Allowed : 8.06 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.73 (0.23), residues: 1326 helix: 1.34 (0.17), residues: 870 sheet: -0.71 (0.55), residues: 54 loop : 1.31 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 117 HIS 0.002 0.000 HIS K 12 PHE 0.008 0.001 PHE E 32 TYR 0.007 0.001 TYR I 169 ARG 0.003 0.001 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 163 time to evaluate : 1.198 Fit side-chains REVERT: A 25 LYS cc_start: 0.8557 (mttt) cc_final: 0.8005 (mttm) REVERT: A 82 ARG cc_start: 0.6870 (ttm170) cc_final: 0.6581 (ttm170) REVERT: A 145 TYR cc_start: 0.7335 (m-80) cc_final: 0.6508 (m-80) REVERT: C 117 TRP cc_start: 0.6246 (m-10) cc_final: 0.5860 (m-10) REVERT: C 144 MET cc_start: 0.7972 (tpp) cc_final: 0.7643 (tpp) REVERT: G 25 LYS cc_start: 0.8554 (mttt) cc_final: 0.7999 (mttm) REVERT: G 82 ARG cc_start: 0.6871 (ttm170) cc_final: 0.6582 (ttm170) REVERT: G 145 TYR cc_start: 0.7337 (m-80) cc_final: 0.6512 (m-80) REVERT: I 117 TRP cc_start: 0.6244 (m-10) cc_final: 0.5860 (m-10) REVERT: I 144 MET cc_start: 0.7970 (tpp) cc_final: 0.7640 (tpp) outliers start: 14 outliers final: 10 residues processed: 171 average time/residue: 0.2552 time to fit residues: 59.4810 Evaluate side-chains 163 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 153 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain I residue 176 GLN Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 74 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 59 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 123 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7153 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10746 Z= 0.221 Angle : 0.565 6.992 14622 Z= 0.292 Chirality : 0.040 0.146 1638 Planarity : 0.005 0.052 1902 Dihedral : 4.659 50.282 1434 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.81 % Favored : 97.74 % Rotamer: Outliers : 1.79 % Allowed : 7.97 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.84 (0.23), residues: 1326 helix: 1.42 (0.17), residues: 870 sheet: -0.61 (0.57), residues: 54 loop : 1.34 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 117 HIS 0.002 0.001 HIS K 12 PHE 0.007 0.001 PHE E 32 TYR 0.007 0.001 TYR C 169 ARG 0.003 0.001 ARG C 162 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 1.218 Fit side-chains REVERT: A 82 ARG cc_start: 0.6885 (ttm170) cc_final: 0.6617 (ttm170) REVERT: A 145 TYR cc_start: 0.7358 (m-80) cc_final: 0.6539 (m-80) REVERT: C 117 TRP cc_start: 0.6160 (m-10) cc_final: 0.5779 (m-10) REVERT: C 144 MET cc_start: 0.7925 (tpp) cc_final: 0.7575 (tpp) REVERT: G 82 ARG cc_start: 0.6886 (ttm170) cc_final: 0.6618 (ttm170) REVERT: G 145 TYR cc_start: 0.7360 (m-80) cc_final: 0.6542 (m-80) REVERT: I 117 TRP cc_start: 0.6153 (m-10) cc_final: 0.5782 (m-10) REVERT: I 144 MET cc_start: 0.7919 (tpp) cc_final: 0.7570 (tpp) REVERT: I 176 GLN cc_start: 0.6342 (OUTLIER) cc_final: 0.6132 (pm20) outliers start: 20 outliers final: 14 residues processed: 158 average time/residue: 0.2581 time to fit residues: 55.4480 Evaluate side-chains 159 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain I residue 176 GLN Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 93 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 77 optimal weight: 0.0470 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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: 0.7156 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10746 Z= 0.226 Angle : 0.554 7.021 14622 Z= 0.286 Chirality : 0.040 0.145 1638 Planarity : 0.005 0.052 1902 Dihedral : 4.629 51.702 1434 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.96 % Favored : 97.59 % Rotamer: Outliers : 1.79 % Allowed : 8.60 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.96 (0.23), residues: 1326 helix: 1.49 (0.17), residues: 864 sheet: -0.51 (0.59), residues: 54 loop : 1.46 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 23 HIS 0.002 0.001 HIS E 12 PHE 0.008 0.001 PHE E 32 TYR 0.007 0.001 TYR I 169 ARG 0.004 0.001 ARG E 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 1.371 Fit side-chains REVERT: A 82 ARG cc_start: 0.6864 (ttm170) cc_final: 0.6602 (ttm170) REVERT: C 117 TRP cc_start: 0.6147 (m-10) cc_final: 0.5853 (m-10) REVERT: G 82 ARG cc_start: 0.6864 (ttm170) cc_final: 0.6600 (ttm170) REVERT: I 117 TRP cc_start: 0.6145 (m-10) cc_final: 0.5856 (m-10) REVERT: I 176 GLN cc_start: 0.6267 (OUTLIER) cc_final: 0.5915 (pm20) outliers start: 20 outliers final: 15 residues processed: 158 average time/residue: 0.2730 time to fit residues: 58.4690 Evaluate side-chains 160 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain I residue 176 GLN Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 24 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 0.0570 chunk 100 optimal weight: 0.5980 chunk 115 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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: 0.7134 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10746 Z= 0.196 Angle : 0.537 6.919 14622 Z= 0.276 Chirality : 0.039 0.141 1638 Planarity : 0.005 0.051 1902 Dihedral : 4.524 52.496 1434 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.66 % Favored : 97.89 % Rotamer: Outliers : 1.34 % Allowed : 9.05 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.98 (0.23), residues: 1326 helix: 1.53 (0.17), residues: 864 sheet: -0.30 (0.60), residues: 54 loop : 1.38 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 23 HIS 0.002 0.000 HIS E 12 PHE 0.008 0.001 PHE K 32 TYR 0.007 0.001 TYR I 169 ARG 0.004 0.001 ARG E 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 143 time to evaluate : 1.263 Fit side-chains REVERT: A 82 ARG cc_start: 0.6890 (ttm170) cc_final: 0.6637 (ttm170) REVERT: C 144 MET cc_start: 0.7842 (tpp) cc_final: 0.7504 (tpt) REVERT: C 145 TYR cc_start: 0.7417 (m-80) cc_final: 0.7152 (m-80) REVERT: E 39 MET cc_start: 0.7149 (tpp) cc_final: 0.6884 (mmt) REVERT: G 82 ARG cc_start: 0.6884 (ttm170) cc_final: 0.6634 (ttm170) REVERT: I 144 MET cc_start: 0.7842 (tpp) cc_final: 0.7508 (tpt) REVERT: I 145 TYR cc_start: 0.7420 (m-80) cc_final: 0.7156 (m-80) REVERT: K 39 MET cc_start: 0.7153 (tpp) cc_final: 0.6894 (mmt) outliers start: 15 outliers final: 9 residues processed: 153 average time/residue: 0.2755 time to fit residues: 56.5637 Evaluate side-chains 145 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 136 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7185 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10746 Z= 0.282 Angle : 0.573 6.737 14622 Z= 0.297 Chirality : 0.041 0.154 1638 Planarity : 0.005 0.052 1902 Dihedral : 4.629 53.900 1434 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.45 % Allowed : 2.11 % Favored : 97.44 % Rotamer: Outliers : 1.25 % Allowed : 9.50 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.84 (0.24), residues: 1326 helix: 1.43 (0.18), residues: 864 sheet: -0.40 (0.60), residues: 54 loop : 1.31 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 23 HIS 0.003 0.001 HIS K 12 PHE 0.008 0.001 PHE K 32 TYR 0.007 0.001 TYR C 169 ARG 0.004 0.001 ARG K 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 144 time to evaluate : 1.154 Fit side-chains REVERT: A 82 ARG cc_start: 0.6865 (ttm170) cc_final: 0.6638 (ttm170) REVERT: A 185 MET cc_start: 0.8090 (mtm) cc_final: 0.7852 (mtt) REVERT: C 144 MET cc_start: 0.7884 (tpp) cc_final: 0.7547 (tpt) REVERT: E 39 MET cc_start: 0.7205 (tpp) cc_final: 0.6915 (mmt) REVERT: E 185 MET cc_start: 0.8129 (mtm) cc_final: 0.7817 (mtt) REVERT: G 82 ARG cc_start: 0.6863 (ttm170) cc_final: 0.6636 (ttm170) REVERT: G 185 MET cc_start: 0.8096 (mtm) cc_final: 0.7839 (mtt) REVERT: I 144 MET cc_start: 0.7885 (tpp) cc_final: 0.7548 (tpt) REVERT: K 39 MET cc_start: 0.7217 (tpp) cc_final: 0.6927 (mmt) REVERT: K 185 MET cc_start: 0.8149 (mtm) cc_final: 0.7839 (mtt) outliers start: 14 outliers final: 12 residues processed: 154 average time/residue: 0.2656 time to fit residues: 55.3483 Evaluate side-chains 170 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 158 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.9980 chunk 87 optimal weight: 0.0670 chunk 131 optimal weight: 0.5980 chunk 121 optimal weight: 0.2980 chunk 104 optimal weight: 0.0970 chunk 10 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 83 optimal weight: 0.4980 chunk 111 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- 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: 0.7118 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10746 Z= 0.168 Angle : 0.526 7.012 14622 Z= 0.272 Chirality : 0.039 0.132 1638 Planarity : 0.005 0.051 1902 Dihedral : 4.522 58.258 1434 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.51 % Favored : 98.04 % Rotamer: Outliers : 1.08 % Allowed : 10.04 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.23), residues: 1326 helix: 1.58 (0.17), residues: 864 sheet: -0.07 (0.61), residues: 54 loop : 1.28 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 23 HIS 0.001 0.000 HIS E 12 PHE 0.010 0.001 PHE E 32 TYR 0.006 0.001 TYR C 169 ARG 0.004 0.000 ARG E 154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 1.193 Fit side-chains REVERT: A 82 ARG cc_start: 0.6857 (ttm170) cc_final: 0.6644 (ttm170) REVERT: A 113 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6580 (tt0) REVERT: A 185 MET cc_start: 0.8010 (mtm) cc_final: 0.7804 (mtt) REVERT: C 144 MET cc_start: 0.7921 (tpp) cc_final: 0.7544 (tpt) REVERT: E 39 MET cc_start: 0.7163 (tpp) cc_final: 0.6904 (mmt) REVERT: G 82 ARG cc_start: 0.6855 (ttm170) cc_final: 0.6641 (ttm170) REVERT: G 113 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6580 (tt0) REVERT: G 185 MET cc_start: 0.8023 (mtm) cc_final: 0.7804 (mtt) REVERT: I 144 MET cc_start: 0.7922 (tpp) cc_final: 0.7547 (tpt) REVERT: K 39 MET cc_start: 0.7171 (tpp) cc_final: 0.6910 (mmt) REVERT: K 185 MET cc_start: 0.8087 (mtm) cc_final: 0.7887 (mtt) outliers start: 12 outliers final: 9 residues processed: 161 average time/residue: 0.2434 time to fit residues: 54.1125 Evaluate side-chains 157 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 148 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.0970 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 107 optimal weight: 0.0670 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 75 optimal weight: 0.0980 overall best weight: 0.2316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.191835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.157705 restraints weight = 10795.126| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.83 r_work: 0.3467 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10746 Z= 0.157 Angle : 0.525 6.887 14622 Z= 0.270 Chirality : 0.039 0.132 1638 Planarity : 0.005 0.049 1902 Dihedral : 4.384 57.978 1434 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.96 % Favored : 97.59 % Rotamer: Outliers : 0.90 % Allowed : 9.95 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.23), residues: 1326 helix: 1.65 (0.17), residues: 870 sheet: 0.09 (0.62), residues: 54 loop : 1.17 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 23 HIS 0.001 0.000 HIS E 12 PHE 0.010 0.001 PHE I 32 TYR 0.007 0.001 TYR G 169 ARG 0.004 0.001 ARG I 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2307.87 seconds wall clock time: 41 minutes 54.61 seconds (2514.61 seconds total)