Starting phenix.real_space_refine on Tue Feb 11 14:28:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8equ_28546/02_2025/8equ_28546_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8equ_28546/02_2025/8equ_28546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8equ_28546/02_2025/8equ_28546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8equ_28546/02_2025/8equ_28546.map" model { file = "/net/cci-nas-00/data/ceres_data/8equ_28546/02_2025/8equ_28546_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8equ_28546/02_2025/8equ_28546_neut.cif" } resolution = 2.8 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= 0.003 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 32 5.16 5 C 3680 2.51 5 N 976 2.21 5 O 1074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5764 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1563 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "C" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 506 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 74} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "E" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 395 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'TRANS': 78} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 79 Planarities with less than four sites: {'UNK:plan-1': 79} Unresolved non-hydrogen planarities: 79 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Restraints were copied for chains: B, D, G, H, F Time building chain proxies: 3.72, per 1000 atoms: 0.65 Number of scatterers: 5764 At special positions: 0 Unit cell: (90.308, 93.684, 89.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 2 15.00 O 1074 8.00 N 976 7.00 C 3680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 521.9 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1668 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 111.8% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 43 through 61 removed outlier: 3.529A pdb=" N ILE A 47 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 99 Processing helix chain 'A' and resid 105 through 134 Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'B' and resid 43 through 61 removed outlier: 3.528A pdb=" N ILE B 47 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 99 Processing helix chain 'B' and resid 105 through 134 Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'C' and resid 2 through 19 removed outlier: 3.502A pdb=" N ILE C 6 " --> pdb=" O LEU C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 37 removed outlier: 3.911A pdb=" N GLU C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 67 removed outlier: 4.298A pdb=" N ASP C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Proline residue: C 56 - end of helix Processing helix chain 'C' and resid 68 through 76 removed outlier: 3.561A pdb=" N LEU C 76 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 19 Processing helix chain 'D' and resid 20 through 36 removed outlier: 3.872A pdb=" N UNK D 24 " --> pdb=" O UNK D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 67 removed outlier: 4.055A pdb=" N UNK D 46 " --> pdb=" O UNK D 42 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N UNK D 56 " --> pdb=" O UNK D 52 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N UNK D 57 " --> pdb=" O UNK D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 76 Processing helix chain 'E' and resid 2 through 19 Processing helix chain 'E' and resid 20 through 36 removed outlier: 3.874A pdb=" N UNK E 24 " --> pdb=" O UNK E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 67 removed outlier: 4.055A pdb=" N UNK E 46 " --> pdb=" O UNK E 42 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N UNK E 56 " --> pdb=" O UNK E 52 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N UNK E 57 " --> pdb=" O UNK E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 76 Processing helix chain 'F' and resid 2 through 19 removed outlier: 3.501A pdb=" N ILE F 6 " --> pdb=" O LEU F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 37 removed outlier: 3.911A pdb=" N GLU F 24 " --> pdb=" O ASP F 20 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS F 35 " --> pdb=" O LEU F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 67 removed outlier: 4.298A pdb=" N ASP F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) Proline residue: F 56 - end of helix Processing helix chain 'F' and resid 68 through 76 removed outlier: 3.560A pdb=" N LEU F 76 " --> pdb=" O VAL F 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 19 Processing helix chain 'G' and resid 20 through 36 removed outlier: 3.873A pdb=" N UNK G 24 " --> pdb=" O UNK G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 67 removed outlier: 4.055A pdb=" N UNK G 46 " --> pdb=" O UNK G 42 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N UNK G 56 " --> pdb=" O UNK G 52 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N UNK G 57 " --> pdb=" O UNK G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 76 Processing helix chain 'H' and resid 2 through 19 Processing helix chain 'H' and resid 20 through 36 removed outlier: 3.874A pdb=" N UNK H 24 " --> pdb=" O UNK H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 67 removed outlier: 4.055A pdb=" N UNK H 46 " --> pdb=" O UNK H 42 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N UNK H 56 " --> pdb=" O UNK H 52 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N UNK H 57 " --> pdb=" O UNK H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 76 Processing sheet with id=AA1, first strand: chain 'A' and resid 155 through 160 removed outlier: 6.193A pdb=" N HIS A 150 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N CYS A 200 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU A 214 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN A 234 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER A 216 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 155 through 160 removed outlier: 6.194A pdb=" N HIS B 150 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N CYS B 200 " --> pdb=" O HIS B 150 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU B 214 " --> pdb=" O ASN B 234 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN B 234 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER B 216 " --> pdb=" O ILE B 232 " (cutoff:3.500A) 506 hydrogen bonds defined for protein. 1500 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 966 1.32 - 1.44: 1530 1.44 - 1.57: 3320 1.57 - 1.70: 4 1.70 - 1.82: 38 Bond restraints: 5858 Sorted by residual: bond pdb=" C10 PEE B 401 " pdb=" O2 PEE B 401 " ideal model delta sigma weight residual 1.332 1.429 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C10 PEE A 401 " pdb=" O2 PEE A 401 " ideal model delta sigma weight residual 1.332 1.428 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C30 PEE A 401 " pdb=" O3 PEE A 401 " ideal model delta sigma weight residual 1.327 1.411 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C30 PEE B 401 " pdb=" O3 PEE B 401 " ideal model delta sigma weight residual 1.327 1.411 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C LEU A 41 " pdb=" N PRO A 42 " ideal model delta sigma weight residual 1.333 1.358 -0.025 1.01e-02 9.80e+03 5.99e+00 ... (remaining 5853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 7999 3.29 - 6.57: 29 6.57 - 9.86: 10 9.86 - 13.15: 0 13.15 - 16.44: 2 Bond angle restraints: 8040 Sorted by residual: angle pdb=" O3P PEE B 401 " pdb=" P PEE B 401 " pdb=" O4P PEE B 401 " ideal model delta sigma weight residual 92.91 109.35 -16.44 3.00e+00 1.11e-01 3.00e+01 angle pdb=" O3P PEE A 401 " pdb=" P PEE A 401 " pdb=" O4P PEE A 401 " ideal model delta sigma weight residual 92.91 109.31 -16.40 3.00e+00 1.11e-01 2.99e+01 angle pdb=" CB MET A 125 " pdb=" CG MET A 125 " pdb=" SD MET A 125 " ideal model delta sigma weight residual 112.70 122.43 -9.73 3.00e+00 1.11e-01 1.05e+01 angle pdb=" CB MET B 125 " pdb=" CG MET B 125 " pdb=" SD MET B 125 " ideal model delta sigma weight residual 112.70 122.40 -9.70 3.00e+00 1.11e-01 1.05e+01 angle pdb=" O1P PEE A 401 " pdb=" P PEE A 401 " pdb=" O2P PEE A 401 " ideal model delta sigma weight residual 119.43 109.80 9.63 3.00e+00 1.11e-01 1.03e+01 ... (remaining 8035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.18: 3355 28.18 - 56.37: 57 56.37 - 84.55: 16 84.55 - 112.73: 0 112.73 - 140.91: 4 Dihedral angle restraints: 3432 sinusoidal: 882 harmonic: 2550 Sorted by residual: dihedral pdb=" CA HIS A 204 " pdb=" C HIS A 204 " pdb=" N SER A 205 " pdb=" CA SER A 205 " ideal model delta harmonic sigma weight residual 180.00 153.40 26.60 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA HIS B 204 " pdb=" C HIS B 204 " pdb=" N SER B 205 " pdb=" CA SER B 205 " ideal model delta harmonic sigma weight residual 180.00 153.42 26.58 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" C3 PEE B 401 " pdb=" C1 PEE B 401 " pdb=" C2 PEE B 401 " pdb=" O3P PEE B 401 " ideal model delta sinusoidal sigma weight residual 62.73 -78.18 140.91 1 3.00e+01 1.11e-03 1.89e+01 ... (remaining 3429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 821 0.048 - 0.096: 159 0.096 - 0.144: 20 0.144 - 0.193: 0 0.193 - 0.241: 2 Chirality restraints: 1002 Sorted by residual: chirality pdb=" C2 PEE A 401 " pdb=" C1 PEE A 401 " pdb=" C3 PEE A 401 " pdb=" O2 PEE A 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.57 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C2 PEE B 401 " pdb=" C1 PEE B 401 " pdb=" C3 PEE B 401 " pdb=" O2 PEE B 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.57 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE A 169 " pdb=" N ILE A 169 " pdb=" C ILE A 169 " pdb=" CB ILE A 169 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 999 not shown) Planarity restraints: 1022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 41 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.54e+00 pdb=" C LEU B 41 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU B 41 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO B 42 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 41 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.53e+00 pdb=" C LEU A 41 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU A 41 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO A 42 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 206 " 0.011 2.00e-02 2.50e+03 1.13e-02 2.55e+00 pdb=" CG TYR B 206 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 206 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 206 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 206 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 206 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 206 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 206 " -0.001 2.00e-02 2.50e+03 ... (remaining 1019 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 26 2.60 - 3.18: 5149 3.18 - 3.75: 9351 3.75 - 4.33: 11343 4.33 - 4.90: 19003 Nonbonded interactions: 44872 Sorted by model distance: nonbonded pdb=" SG CYS C 35 " pdb=" SG CYS C 47 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS F 35 " pdb=" SG CYS F 47 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS C 7 " pdb=" SG CYS C 73 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS C 4 " pdb=" SG CYS C 79 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS F 7 " pdb=" SG CYS F 73 " model vdw 2.032 3.760 ... (remaining 44867 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.450 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 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 : 0.004 0.097 5858 Z= 0.260 Angle : 0.790 16.435 8040 Z= 0.382 Chirality : 0.040 0.241 1002 Planarity : 0.004 0.032 1022 Dihedral : 14.512 140.915 1764 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.36), residues: 530 helix: 0.76 (0.30), residues: 308 sheet: -0.26 (0.51), residues: 92 loop : -1.82 (0.49), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 193 HIS 0.004 0.001 HIS A 204 PHE 0.010 0.001 PHE B 56 TYR 0.028 0.002 TYR B 206 ARG 0.003 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7786 (mpp80) cc_final: 0.7553 (mpp80) REVERT: A 198 LYS cc_start: 0.7882 (mtpt) cc_final: 0.7624 (mmmm) REVERT: A 210 ASP cc_start: 0.8189 (m-30) cc_final: 0.7947 (m-30) REVERT: A 213 GLN cc_start: 0.7923 (tt0) cc_final: 0.7377 (tp40) REVERT: B 198 LYS cc_start: 0.7917 (mtpt) cc_final: 0.7628 (mmmm) REVERT: B 210 ASP cc_start: 0.8185 (m-30) cc_final: 0.7924 (m-30) REVERT: B 211 TYR cc_start: 0.8528 (m-80) cc_final: 0.8273 (m-80) REVERT: B 213 GLN cc_start: 0.7932 (tt0) cc_final: 0.7353 (tp40) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.8534 time to fit residues: 89.6770 Evaluate side-chains 75 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 47 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 HIS ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS F 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.186763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.107637 restraints weight = 7069.747| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.48 r_work: 0.2958 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.064 5858 Z= 0.595 Angle : 0.679 8.454 8040 Z= 0.341 Chirality : 0.042 0.161 1002 Planarity : 0.004 0.040 1022 Dihedral : 9.753 99.876 928 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.93 % Allowed : 12.38 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.35), residues: 530 helix: 1.08 (0.28), residues: 318 sheet: -0.63 (0.50), residues: 90 loop : -1.80 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 149 HIS 0.005 0.002 HIS B 78 PHE 0.026 0.004 PHE A 43 TYR 0.029 0.003 TYR B 215 ARG 0.004 0.001 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.575 Fit side-chains REVERT: A 61 LYS cc_start: 0.8841 (mttm) cc_final: 0.8433 (mtpt) REVERT: A 128 TRP cc_start: 0.8574 (t60) cc_final: 0.8229 (t60) REVERT: A 213 GLN cc_start: 0.8675 (tt0) cc_final: 0.8459 (tt0) REVERT: B 61 LYS cc_start: 0.8809 (mttm) cc_final: 0.8423 (mtpt) REVERT: B 128 TRP cc_start: 0.8567 (t60) cc_final: 0.8197 (t60) REVERT: B 155 ASP cc_start: 0.8399 (m-30) cc_final: 0.8196 (m-30) REVERT: B 213 GLN cc_start: 0.8682 (tt0) cc_final: 0.8464 (tt0) outliers start: 4 outliers final: 3 residues processed: 86 average time/residue: 0.9766 time to fit residues: 88.7228 Evaluate side-chains 79 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 222 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 57 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 54 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 51 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.184158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.105460 restraints weight = 7137.643| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.43 r_work: 0.2945 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.074 5858 Z= 0.679 Angle : 0.688 9.113 8040 Z= 0.347 Chirality : 0.044 0.200 1002 Planarity : 0.004 0.043 1022 Dihedral : 9.932 98.956 928 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.87 % Allowed : 15.89 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.35), residues: 530 helix: 0.92 (0.28), residues: 318 sheet: -0.94 (0.49), residues: 90 loop : -2.02 (0.49), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 149 HIS 0.007 0.002 HIS B 78 PHE 0.016 0.003 PHE B 146 TYR 0.016 0.002 TYR A 109 ARG 0.005 0.001 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.546 Fit side-chains REVERT: A 128 TRP cc_start: 0.8659 (t60) cc_final: 0.8387 (t60) REVERT: A 155 ASP cc_start: 0.8543 (m-30) cc_final: 0.8073 (m-30) REVERT: A 182 HIS cc_start: 0.7511 (m-70) cc_final: 0.7241 (m90) REVERT: A 213 GLN cc_start: 0.8657 (tt0) cc_final: 0.8410 (tt0) REVERT: B 128 TRP cc_start: 0.8681 (t60) cc_final: 0.8394 (t60) REVERT: B 182 HIS cc_start: 0.7457 (m-70) cc_final: 0.7229 (m90) REVERT: B 194 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8191 (mm-30) REVERT: B 213 GLN cc_start: 0.8638 (tt0) cc_final: 0.8386 (tt0) outliers start: 8 outliers final: 5 residues processed: 84 average time/residue: 1.0243 time to fit residues: 90.6622 Evaluate side-chains 74 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 222 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 34 optimal weight: 0.9980 chunk 75 optimal weight: 30.0000 chunk 59 optimal weight: 30.0000 chunk 46 optimal weight: 30.0000 chunk 10 optimal weight: 0.7980 chunk 74 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 60 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 78 HIS B 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.186281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107733 restraints weight = 7197.623| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.45 r_work: 0.2984 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5858 Z= 0.353 Angle : 0.563 7.646 8040 Z= 0.281 Chirality : 0.036 0.148 1002 Planarity : 0.004 0.042 1022 Dihedral : 9.393 92.534 928 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.04 % Allowed : 15.65 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.35), residues: 530 helix: 1.20 (0.29), residues: 318 sheet: -1.04 (0.50), residues: 90 loop : -2.01 (0.47), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 149 HIS 0.003 0.001 HIS B 78 PHE 0.012 0.002 PHE A 146 TYR 0.011 0.002 TYR B 206 ARG 0.004 0.001 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.414 Fit side-chains REVERT: A 128 TRP cc_start: 0.8608 (t60) cc_final: 0.8249 (t60) REVERT: A 182 HIS cc_start: 0.7575 (m-70) cc_final: 0.7367 (m90) REVERT: A 213 GLN cc_start: 0.8614 (tt0) cc_final: 0.8395 (tt0) REVERT: B 128 TRP cc_start: 0.8608 (t60) cc_final: 0.8249 (t60) REVERT: B 182 HIS cc_start: 0.7515 (m-70) cc_final: 0.7301 (m90) REVERT: B 213 GLN cc_start: 0.8620 (tt0) cc_final: 0.8402 (tt0) outliers start: 13 outliers final: 8 residues processed: 80 average time/residue: 0.9908 time to fit residues: 83.6380 Evaluate side-chains 80 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain F residue 62 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 55 optimal weight: 30.0000 chunk 34 optimal weight: 0.8980 chunk 47 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 53 optimal weight: 30.0000 chunk 18 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 56 optimal weight: 20.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN B 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.187715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.111292 restraints weight = 7054.296| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.39 r_work: 0.3034 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5858 Z= 0.224 Angle : 0.521 7.784 8040 Z= 0.258 Chirality : 0.035 0.151 1002 Planarity : 0.003 0.039 1022 Dihedral : 8.736 85.864 928 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.57 % Allowed : 17.06 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.36), residues: 530 helix: 1.53 (0.29), residues: 318 sheet: -1.07 (0.52), residues: 90 loop : -2.00 (0.48), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 149 HIS 0.003 0.001 HIS A 204 PHE 0.010 0.002 PHE B 56 TYR 0.013 0.001 TYR A 154 ARG 0.004 0.001 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.536 Fit side-chains REVERT: A 128 TRP cc_start: 0.8542 (t60) cc_final: 0.8168 (t60) REVERT: A 155 ASP cc_start: 0.8453 (m-30) cc_final: 0.8019 (m-30) REVERT: A 213 GLN cc_start: 0.8632 (tt0) cc_final: 0.8372 (tt0) REVERT: B 128 TRP cc_start: 0.8546 (t60) cc_final: 0.8163 (t60) REVERT: B 134 ARG cc_start: 0.8213 (mmm-85) cc_final: 0.7970 (mmm-85) REVERT: B 150 HIS cc_start: 0.7770 (m-70) cc_final: 0.7416 (m-70) REVERT: B 213 GLN cc_start: 0.8637 (tt0) cc_final: 0.8373 (tt0) outliers start: 11 outliers final: 9 residues processed: 87 average time/residue: 0.8429 time to fit residues: 78.3026 Evaluate side-chains 79 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain F residue 62 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 30.0000 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 52 optimal weight: 30.0000 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 68 optimal weight: 20.0000 chunk 3 optimal weight: 0.6980 chunk 79 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.188206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.110377 restraints weight = 7148.176| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.46 r_work: 0.3032 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5858 Z= 0.223 Angle : 0.525 8.334 8040 Z= 0.258 Chirality : 0.035 0.160 1002 Planarity : 0.003 0.038 1022 Dihedral : 8.240 81.550 928 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.04 % Allowed : 18.93 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.36), residues: 530 helix: 1.69 (0.29), residues: 318 sheet: -1.06 (0.52), residues: 90 loop : -1.97 (0.48), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 149 HIS 0.002 0.001 HIS A 93 PHE 0.010 0.002 PHE B 56 TYR 0.012 0.001 TYR A 154 ARG 0.004 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.546 Fit side-chains REVERT: A 128 TRP cc_start: 0.8501 (t60) cc_final: 0.8099 (t60) REVERT: A 213 GLN cc_start: 0.8635 (tt0) cc_final: 0.8367 (tt0) REVERT: B 128 TRP cc_start: 0.8523 (t60) cc_final: 0.8112 (t60) REVERT: B 134 ARG cc_start: 0.8246 (mmm-85) cc_final: 0.7946 (mmm-85) REVERT: B 150 HIS cc_start: 0.7843 (m-70) cc_final: 0.7556 (m-70) REVERT: B 213 GLN cc_start: 0.8619 (tt0) cc_final: 0.8346 (tt0) outliers start: 13 outliers final: 7 residues processed: 84 average time/residue: 0.8292 time to fit residues: 74.3606 Evaluate side-chains 79 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain F residue 62 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 47 optimal weight: 20.0000 chunk 22 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 37 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4249 r_free = 0.4249 target = 0.186923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.109513 restraints weight = 7111.219| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.42 r_work: 0.3006 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5858 Z= 0.307 Angle : 0.561 9.114 8040 Z= 0.274 Chirality : 0.036 0.168 1002 Planarity : 0.003 0.038 1022 Dihedral : 8.023 80.813 928 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.10 % Allowed : 20.09 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.36), residues: 530 helix: 1.71 (0.29), residues: 318 sheet: -1.10 (0.51), residues: 90 loop : -1.95 (0.48), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 131 HIS 0.002 0.001 HIS A 78 PHE 0.010 0.002 PHE B 56 TYR 0.014 0.001 TYR A 154 ARG 0.003 0.001 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.520 Fit side-chains REVERT: A 128 TRP cc_start: 0.8596 (t60) cc_final: 0.8226 (t60) REVERT: A 155 ASP cc_start: 0.8441 (m-30) cc_final: 0.8026 (m-30) REVERT: A 213 GLN cc_start: 0.8653 (tt0) cc_final: 0.8392 (tt0) REVERT: B 128 TRP cc_start: 0.8595 (t60) cc_final: 0.8222 (t60) REVERT: B 134 ARG cc_start: 0.8253 (mmm-85) cc_final: 0.7947 (mmm-85) REVERT: B 150 HIS cc_start: 0.7852 (m-70) cc_final: 0.7573 (m-70) REVERT: B 213 GLN cc_start: 0.8652 (tt0) cc_final: 0.8388 (tt0) outliers start: 9 outliers final: 8 residues processed: 78 average time/residue: 0.8717 time to fit residues: 72.6712 Evaluate side-chains 77 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain F residue 62 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 1 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 78 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 28 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 70 optimal weight: 20.0000 chunk 77 optimal weight: 30.0000 chunk 44 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4260 r_free = 0.4260 target = 0.188112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.111666 restraints weight = 7001.259| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.40 r_work: 0.3045 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5858 Z= 0.210 Angle : 0.536 9.567 8040 Z= 0.260 Chirality : 0.035 0.169 1002 Planarity : 0.003 0.038 1022 Dihedral : 7.714 76.928 928 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.80 % Allowed : 19.86 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.36), residues: 530 helix: 2.01 (0.29), residues: 306 sheet: -1.10 (0.52), residues: 90 loop : -1.66 (0.46), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 131 HIS 0.002 0.001 HIS B 93 PHE 0.010 0.001 PHE B 56 TYR 0.012 0.001 TYR A 109 ARG 0.004 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.516 Fit side-chains REVERT: A 128 TRP cc_start: 0.8545 (t60) cc_final: 0.8182 (t60) REVERT: A 155 ASP cc_start: 0.8406 (m-30) cc_final: 0.8077 (m-30) REVERT: A 213 GLN cc_start: 0.8634 (tt0) cc_final: 0.8366 (tt0) REVERT: B 128 TRP cc_start: 0.8532 (t60) cc_final: 0.8125 (t60) REVERT: B 134 ARG cc_start: 0.8257 (mmm-85) cc_final: 0.7971 (mmm-85) REVERT: B 213 GLN cc_start: 0.8629 (tt0) cc_final: 0.8358 (tt0) REVERT: F 8 LYS cc_start: 0.7591 (mttt) cc_final: 0.6948 (mmtp) outliers start: 12 outliers final: 8 residues processed: 77 average time/residue: 0.8318 time to fit residues: 68.3105 Evaluate side-chains 74 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain F residue 62 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 45 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 28 optimal weight: 0.7980 chunk 76 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 chunk 39 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.186959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.111319 restraints weight = 7001.175| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.44 r_work: 0.3029 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5858 Z= 0.276 Angle : 0.570 9.304 8040 Z= 0.276 Chirality : 0.036 0.174 1002 Planarity : 0.003 0.038 1022 Dihedral : 7.522 74.660 928 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.04 % Allowed : 19.63 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.37), residues: 530 helix: 1.83 (0.29), residues: 318 sheet: -1.17 (0.52), residues: 90 loop : -1.87 (0.50), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 131 HIS 0.003 0.001 HIS B 150 PHE 0.010 0.002 PHE B 56 TYR 0.012 0.001 TYR A 109 ARG 0.003 0.001 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.504 Fit side-chains REVERT: A 128 TRP cc_start: 0.8620 (t60) cc_final: 0.8244 (t60) REVERT: A 155 ASP cc_start: 0.8432 (m-30) cc_final: 0.8020 (m-30) REVERT: A 213 GLN cc_start: 0.8650 (tt0) cc_final: 0.8388 (tt0) REVERT: B 128 TRP cc_start: 0.8588 (t60) cc_final: 0.8208 (t60) REVERT: B 134 ARG cc_start: 0.8211 (mmm-85) cc_final: 0.7968 (mmm-85) REVERT: B 213 GLN cc_start: 0.8649 (tt0) cc_final: 0.8384 (tt0) REVERT: C 8 LYS cc_start: 0.7728 (mttt) cc_final: 0.7064 (mtpp) REVERT: F 8 LYS cc_start: 0.7650 (mttt) cc_final: 0.6951 (mmtp) outliers start: 13 outliers final: 9 residues processed: 77 average time/residue: 0.9371 time to fit residues: 76.5319 Evaluate side-chains 77 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain C residue 62 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 67 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 81 optimal weight: 20.0000 chunk 37 optimal weight: 0.5980 chunk 70 optimal weight: 20.0000 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.0010 chunk 4 optimal weight: 0.0970 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 overall best weight: 0.3984 ------------------------------------------------------------------------------- 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 = 0.4265 r_free = 0.4265 target = 0.188948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.113791 restraints weight = 7069.244| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.48 r_work: 0.3059 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5858 Z= 0.166 Angle : 0.561 13.107 8040 Z= 0.264 Chirality : 0.035 0.165 1002 Planarity : 0.003 0.036 1022 Dihedral : 7.172 68.420 928 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.64 % Allowed : 21.73 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.37), residues: 530 helix: 1.98 (0.29), residues: 318 sheet: -1.07 (0.52), residues: 90 loop : -1.84 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 131 HIS 0.003 0.001 HIS A 204 PHE 0.010 0.001 PHE B 56 TYR 0.009 0.001 TYR A 154 ARG 0.004 0.001 ARG A 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.515 Fit side-chains REVERT: A 127 LEU cc_start: 0.8802 (mm) cc_final: 0.8596 (mm) REVERT: A 128 TRP cc_start: 0.8380 (t60) cc_final: 0.7972 (t60) REVERT: A 155 ASP cc_start: 0.8361 (m-30) cc_final: 0.7996 (m-30) REVERT: A 213 GLN cc_start: 0.8483 (tt0) cc_final: 0.8199 (tt0) REVERT: B 128 TRP cc_start: 0.8396 (t60) cc_final: 0.8004 (t60) REVERT: B 213 GLN cc_start: 0.8482 (tt0) cc_final: 0.8198 (tt0) REVERT: C 8 LYS cc_start: 0.7584 (mttt) cc_final: 0.6945 (mtpp) REVERT: F 8 LYS cc_start: 0.7602 (mttt) cc_final: 0.6874 (mmtm) outliers start: 7 outliers final: 7 residues processed: 73 average time/residue: 0.8901 time to fit residues: 69.1571 Evaluate side-chains 76 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain F residue 62 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 61 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 32 optimal weight: 0.4980 chunk 9 optimal weight: 0.1980 chunk 13 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.188658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.114390 restraints weight = 7067.659| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.45 r_work: 0.3065 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5858 Z= 0.176 Angle : 0.557 12.382 8040 Z= 0.263 Chirality : 0.035 0.170 1002 Planarity : 0.003 0.036 1022 Dihedral : 6.826 63.364 928 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.64 % Allowed : 21.73 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.37), residues: 530 helix: 2.09 (0.29), residues: 318 sheet: -1.12 (0.52), residues: 90 loop : -1.89 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 131 HIS 0.002 0.001 HIS B 204 PHE 0.010 0.001 PHE B 56 TYR 0.009 0.001 TYR A 154 ARG 0.004 0.001 ARG A 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5376.36 seconds wall clock time: 95 minutes 30.84 seconds (5730.84 seconds total)