Starting phenix.real_space_refine on Mon Jun 24 17:18:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve1_43161/06_2024/8ve1_43161_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve1_43161/06_2024/8ve1_43161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve1_43161/06_2024/8ve1_43161.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve1_43161/06_2024/8ve1_43161.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve1_43161/06_2024/8ve1_43161_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve1_43161/06_2024/8ve1_43161_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 8 5.16 5 C 2331 2.51 5 N 592 2.21 5 O 725 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 54": "OE1" <-> "OE2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 39": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 3656 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 899 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 891 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 108} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 901 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 109} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'1WZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'1WZ:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'1WZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'1WZ:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 2.54, per 1000 atoms: 0.69 Number of scatterers: 3656 At special positions: 0 Unit cell: (80.366, 65.754, 54.514, 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 8 16.00 O 725 8.00 N 592 7.00 C 2331 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 637.3 milliseconds 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 876 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 4 helices and 8 sheets defined 6.7% alpha, 39.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 75 through 82 Processing helix chain 'B' and resid 75 through 82 removed outlier: 3.729A pdb=" N LEU B 82 " --> pdb=" O TYR B 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 82 Processing helix chain 'D' and resid 75 through 81 Processing sheet with id= A, first strand: chain 'A' and resid 12 through 18 removed outlier: 8.241A pdb=" N MET A 13 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TYR A 105 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LYS A 15 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE A 107 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU A 17 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ALA A 109 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 91 through 97 removed outlier: 5.271A pdb=" N ILE A 68 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ARG A 34 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 12 through 18 removed outlier: 6.319A pdb=" N TYR B 105 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LYS B 15 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE B 107 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU B 17 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ALA B 109 " --> pdb=" O LEU B 17 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 91 through 97 removed outlier: 5.454A pdb=" N ILE B 68 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ARG B 34 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 12 through 18 removed outlier: 6.424A pdb=" N TYR C 105 " --> pdb=" O MET C 13 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LYS C 15 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE C 107 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LEU C 17 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA C 109 " --> pdb=" O LEU C 17 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 91 through 97 removed outlier: 5.633A pdb=" N ILE C 68 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ARG C 34 " --> pdb=" O PRO C 43 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 12 through 18 removed outlier: 6.405A pdb=" N TYR D 105 " --> pdb=" O MET D 13 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LYS D 15 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE D 107 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU D 17 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA D 109 " --> pdb=" O LEU D 17 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 91 through 97 removed outlier: 5.515A pdb=" N ILE D 68 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ARG D 34 " --> pdb=" O PRO D 43 " (cutoff:3.500A) 114 hydrogen bonds defined for protein. 309 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.89 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 598 1.31 - 1.43: 1027 1.43 - 1.56: 2087 1.56 - 1.68: 2 1.68 - 1.81: 12 Bond restraints: 3726 Sorted by residual: bond pdb=" CAH 1WZ C 201 " pdb=" CAR 1WZ C 201 " ideal model delta sigma weight residual 1.461 1.568 -0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" CAH 1WZ B 201 " pdb=" CAR 1WZ B 201 " ideal model delta sigma weight residual 1.461 1.567 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" CAV 1WZ B 201 " pdb=" NAW 1WZ B 201 " ideal model delta sigma weight residual 1.376 1.471 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" CAV 1WZ C 201 " pdb=" NAW 1WZ C 201 " ideal model delta sigma weight residual 1.376 1.470 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C LYS C 15 " pdb=" O LYS C 15 " ideal model delta sigma weight residual 1.236 1.181 0.055 1.19e-02 7.06e+03 2.14e+01 ... (remaining 3721 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.15: 143 107.15 - 113.87: 2099 113.87 - 120.59: 1390 120.59 - 127.30: 1403 127.30 - 134.02: 53 Bond angle restraints: 5088 Sorted by residual: angle pdb=" CAH 1WZ B 201 " pdb=" CAI 1WZ B 201 " pdb=" CAS 1WZ B 201 " ideal model delta sigma weight residual 126.24 115.58 10.66 3.00e+00 1.11e-01 1.26e+01 angle pdb=" CA LYS B 15 " pdb=" CB LYS B 15 " pdb=" CG LYS B 15 " ideal model delta sigma weight residual 114.10 107.17 6.93 2.00e+00 2.50e-01 1.20e+01 angle pdb=" CAH 1WZ C 201 " pdb=" CAI 1WZ C 201 " pdb=" CAS 1WZ C 201 " ideal model delta sigma weight residual 126.24 116.87 9.37 3.00e+00 1.11e-01 9.76e+00 angle pdb=" CAI 1WZ C 201 " pdb=" CAH 1WZ C 201 " pdb=" CAR 1WZ C 201 " ideal model delta sigma weight residual 126.51 118.59 7.92 3.00e+00 1.11e-01 6.98e+00 angle pdb=" CA LYS C 15 " pdb=" CB LYS C 15 " pdb=" CG LYS C 15 " ideal model delta sigma weight residual 114.10 109.12 4.98 2.00e+00 2.50e-01 6.19e+00 ... (remaining 5083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 1952 15.63 - 31.26: 164 31.26 - 46.88: 39 46.88 - 62.51: 9 62.51 - 78.14: 4 Dihedral angle restraints: 2168 sinusoidal: 810 harmonic: 1358 Sorted by residual: dihedral pdb=" CA ALA C 91 " pdb=" C ALA C 91 " pdb=" N GLU C 92 " pdb=" CA GLU C 92 " ideal model delta harmonic sigma weight residual 180.00 -161.67 -18.33 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CB LYS B 15 " pdb=" CG LYS B 15 " pdb=" CD LYS B 15 " pdb=" CE LYS B 15 " ideal model delta sinusoidal sigma weight residual 60.00 116.93 -56.93 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CG LYS A 80 " pdb=" CD LYS A 80 " pdb=" CE LYS A 80 " pdb=" NZ LYS A 80 " ideal model delta sinusoidal sigma weight residual -180.00 -127.10 -52.90 3 1.50e+01 4.44e-03 9.16e+00 ... (remaining 2165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 285 0.024 - 0.048: 159 0.048 - 0.071: 60 0.071 - 0.095: 9 0.095 - 0.119: 60 Chirality restraints: 573 Sorted by residual: chirality pdb=" CA ILE A 73 " pdb=" N ILE A 73 " pdb=" C ILE A 73 " pdb=" CB ILE A 73 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.53e-01 chirality pdb=" CA ILE D 73 " pdb=" N ILE D 73 " pdb=" C ILE D 73 " pdb=" CB ILE D 73 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.52e-01 chirality pdb=" CA ILE B 107 " pdb=" N ILE B 107 " pdb=" C ILE B 107 " pdb=" CB ILE B 107 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.49e-01 ... (remaining 570 not shown) Planarity restraints: 648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 112 " 0.019 5.00e-02 4.00e+02 2.94e-02 1.38e+00 pdb=" N PRO D 113 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO D 113 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 113 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 92 " -0.005 2.00e-02 2.50e+03 1.10e-02 1.20e+00 pdb=" CD GLU C 92 " 0.019 2.00e-02 2.50e+03 pdb=" OE1 GLU C 92 " -0.007 2.00e-02 2.50e+03 pdb=" OE2 GLU C 92 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 112 " -0.015 5.00e-02 4.00e+02 2.29e-02 8.35e-01 pdb=" N PRO C 113 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO C 113 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 113 " -0.013 5.00e-02 4.00e+02 ... (remaining 645 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 776 2.79 - 3.31: 3106 3.31 - 3.84: 6276 3.84 - 4.37: 7448 4.37 - 4.90: 13203 Nonbonded interactions: 30809 Sorted by model distance: nonbonded pdb=" O HIS A 90 " pdb=" O HOH A 201 " model vdw 2.258 2.440 nonbonded pdb=" OG SER C 52 " pdb=" OE1 GLU C 54 " model vdw 2.312 2.440 nonbonded pdb=" O ASN C 27 " pdb=" O HOH C 301 " model vdw 2.318 2.440 nonbonded pdb=" O HIS B 88 " pdb=" O HOH B 301 " model vdw 2.335 2.440 nonbonded pdb=" NH1 ARG D 34 " pdb=" OE2 GLU D 42 " model vdw 2.337 2.520 ... (remaining 30804 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 91 or (resid 92 and (name N or name CA or name \ C or name O or name CB )) or resid 93 through 99 or (resid 100 and (name N or na \ me CA or name C or name O or name CB )) or resid 101 through 124)) selection = (chain 'B' and (resid 10 through 58 or (resid 59 and (name N or name CA or name \ C or name O or name CB )) or resid 60 through 124)) selection = (chain 'C' and (resid 10 through 58 or (resid 59 and (name N or name CA or name \ C or name O or name CB )) or resid 60 through 91 or (resid 92 and (name N or nam \ e CA or name C or name O or name CB )) or resid 93 through 99 or (resid 100 and \ (name N or name CA or name C or name O or name CB )) or resid 101 through 124)) selection = (chain 'D' and (resid 10 through 58 or (resid 59 and (name N or name CA or name \ C or name O or name CB )) or resid 60 through 91 or (resid 92 and (name N or nam \ e CA or name C or name O or name CB )) or resid 93 through 99 or (resid 100 and \ (name N or name CA or name C or name O or name CB )) or resid 101 through 124)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.340 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.000 Find NCS groups from input model: 0.270 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:13.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 3726 Z= 0.362 Angle : 0.583 10.659 5088 Z= 0.278 Chirality : 0.046 0.119 573 Planarity : 0.003 0.029 648 Dihedral : 13.153 78.141 1292 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.26 % Allowed : 0.52 % Favored : 99.22 % 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: 0.62 (0.39), residues: 458 helix: -0.53 (0.80), residues: 34 sheet: 1.33 (0.32), residues: 239 loop : -0.64 (0.46), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 41 HIS 0.001 0.000 HIS B 56 PHE 0.014 0.001 PHE C 64 TYR 0.010 0.001 TYR D 116 ARG 0.002 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.386 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 1.3343 time to fit residues: 113.6597 Evaluate side-chains 74 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 0.0170 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3726 Z= 0.203 Angle : 0.503 5.915 5088 Z= 0.263 Chirality : 0.047 0.147 573 Planarity : 0.003 0.029 648 Dihedral : 6.272 67.917 504 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.86 % Allowed : 9.64 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.38), residues: 458 helix: -0.13 (0.85), residues: 36 sheet: 1.28 (0.32), residues: 231 loop : -0.82 (0.42), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 41 HIS 0.001 0.000 HIS C 90 PHE 0.009 0.001 PHE C 64 TYR 0.010 0.001 TYR D 116 ARG 0.001 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.363 Fit side-chains REVERT: C 13 MET cc_start: 0.7190 (tmm) cc_final: 0.6921 (tmt) outliers start: 11 outliers final: 7 residues processed: 86 average time/residue: 1.3986 time to fit residues: 123.3856 Evaluate side-chains 86 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 48 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3726 Z= 0.270 Angle : 0.552 6.985 5088 Z= 0.281 Chirality : 0.048 0.147 573 Planarity : 0.003 0.030 648 Dihedral : 6.341 59.729 504 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.12 % Allowed : 12.76 % Favored : 84.11 % 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: 0.28 (0.37), residues: 458 helix: 0.16 (0.86), residues: 34 sheet: 1.05 (0.31), residues: 238 loop : -0.96 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 41 HIS 0.001 0.000 HIS B 88 PHE 0.009 0.001 PHE C 64 TYR 0.011 0.001 TYR D 116 ARG 0.003 0.000 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: B 80 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7620 (mptp) outliers start: 12 outliers final: 9 residues processed: 83 average time/residue: 1.4623 time to fit residues: 124.3968 Evaluate side-chains 88 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 48 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 3726 Z= 0.439 Angle : 0.627 7.288 5088 Z= 0.322 Chirality : 0.050 0.148 573 Planarity : 0.004 0.034 648 Dihedral : 6.291 47.317 504 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.17 % Allowed : 14.06 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.37), residues: 458 helix: -0.13 (0.83), residues: 34 sheet: 0.89 (0.32), residues: 235 loop : -1.26 (0.41), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 41 HIS 0.003 0.001 HIS B 88 PHE 0.012 0.002 PHE A 33 TYR 0.012 0.002 TYR D 116 ARG 0.003 0.001 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7658 (mptp) REVERT: C 13 MET cc_start: 0.7193 (tmm) cc_final: 0.6977 (ttt) outliers start: 16 outliers final: 11 residues processed: 83 average time/residue: 1.5457 time to fit residues: 131.3626 Evaluate side-chains 93 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 72 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3726 Z= 0.217 Angle : 0.495 5.290 5088 Z= 0.255 Chirality : 0.047 0.141 573 Planarity : 0.004 0.032 648 Dihedral : 5.615 50.142 504 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.65 % Allowed : 14.84 % Favored : 81.51 % 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: -0.13 (0.37), residues: 458 helix: -0.21 (0.82), residues: 36 sheet: 0.73 (0.32), residues: 226 loop : -1.03 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 41 HIS 0.001 0.000 HIS B 88 PHE 0.007 0.001 PHE C 33 TYR 0.009 0.001 TYR D 116 ARG 0.003 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 88 average time/residue: 1.4845 time to fit residues: 133.8365 Evaluate side-chains 93 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 54 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 3726 Z= 0.522 Angle : 0.672 7.851 5088 Z= 0.349 Chirality : 0.052 0.145 573 Planarity : 0.005 0.041 648 Dihedral : 6.190 49.578 504 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.95 % Allowed : 15.10 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.37), residues: 458 helix: -0.46 (0.81), residues: 34 sheet: 0.70 (0.31), residues: 235 loop : -1.44 (0.41), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 41 HIS 0.003 0.001 HIS B 88 PHE 0.012 0.002 PHE A 33 TYR 0.012 0.002 TYR D 116 ARG 0.003 0.001 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: B 42 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7577 (pp20) REVERT: B 80 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7663 (mptp) outliers start: 19 outliers final: 10 residues processed: 82 average time/residue: 1.4848 time to fit residues: 124.6865 Evaluate side-chains 88 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 54 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 23 optimal weight: 0.3980 chunk 42 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3726 Z= 0.187 Angle : 0.513 4.835 5088 Z= 0.263 Chirality : 0.047 0.142 573 Planarity : 0.004 0.032 648 Dihedral : 7.080 82.986 504 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 3.91 % Allowed : 16.67 % Favored : 79.43 % 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: 458 helix: -0.28 (0.81), residues: 36 sheet: 0.47 (0.32), residues: 222 loop : -1.07 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 41 HIS 0.001 0.000 HIS B 88 PHE 0.008 0.001 PHE C 33 TYR 0.008 0.001 TYR D 116 ARG 0.004 0.000 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: B 80 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7492 (mptp) outliers start: 15 outliers final: 7 residues processed: 85 average time/residue: 1.4462 time to fit residues: 126.0593 Evaluate side-chains 88 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 54 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 0.4980 chunk 37 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3726 Z= 0.258 Angle : 0.560 7.190 5088 Z= 0.284 Chirality : 0.048 0.142 573 Planarity : 0.004 0.032 648 Dihedral : 6.914 70.566 504 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.12 % Allowed : 17.97 % Favored : 78.91 % 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: -0.33 (0.36), residues: 458 helix: -0.25 (0.82), residues: 36 sheet: 0.55 (0.32), residues: 226 loop : -1.11 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 41 HIS 0.002 0.000 HIS B 88 PHE 0.008 0.001 PHE A 33 TYR 0.011 0.001 TYR D 116 ARG 0.004 0.000 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7501 (mptp) outliers start: 12 outliers final: 8 residues processed: 82 average time/residue: 1.5091 time to fit residues: 126.7370 Evaluate side-chains 87 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 54 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.8753 > 50: distance: 7 - 146: 36.496 distance: 10 - 143: 36.822 distance: 23 - 135: 33.493 distance: 26 - 132: 33.057 distance: 65 - 68: 28.436 distance: 69 - 70: 22.728 distance: 69 - 72: 17.295 distance: 70 - 76: 4.000 distance: 72 - 73: 3.918 distance: 73 - 74: 14.856 distance: 73 - 75: 29.184 distance: 76 - 77: 3.566 distance: 77 - 80: 40.103 distance: 80 - 81: 40.120 distance: 92 - 95: 3.989 distance: 93 - 105: 37.551 distance: 96 - 97: 39.619 distance: 98 - 100: 40.273 distance: 103 - 104: 40.253 distance: 106 - 107: 38.877 distance: 106 - 109: 57.283 distance: 111 - 112: 40.002 distance: 111 - 113: 24.966 distance: 116 - 117: 39.315 distance: 118 - 119: 4.529 distance: 119 - 120: 3.799 distance: 123 - 132: 39.605 distance: 126 - 127: 39.769 distance: 126 - 128: 40.514 distance: 129 - 131: 40.518 distance: 130 - 131: 39.774 distance: 132 - 133: 41.107 distance: 133 - 134: 32.827 distance: 134 - 135: 10.151 distance: 134 - 137: 9.094 distance: 137 - 138: 32.016 distance: 138 - 139: 41.131 distance: 138 - 141: 11.104 distance: 139 - 140: 40.466 distance: 139 - 143: 38.819 distance: 141 - 142: 29.035 distance: 143 - 144: 39.457 distance: 144 - 145: 69.490 distance: 145 - 147: 34.252