Starting phenix.real_space_refine on Sun Mar 10 21:05:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epa_28523/03_2024/8epa_28523.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epa_28523/03_2024/8epa_28523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epa_28523/03_2024/8epa_28523.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epa_28523/03_2024/8epa_28523.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epa_28523/03_2024/8epa_28523.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epa_28523/03_2024/8epa_28523.pdb" } resolution = 3.4 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= 0.012 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 24 5.16 5 C 3179 2.51 5 N 872 2.21 5 O 970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I GLU 149": "OE1" <-> "OE2" Residue "I PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 17": "OD1" <-> "OD2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 105": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5045 Number of models: 1 Model: "" Number of chains: 6 Chain: "I" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1580 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 173} Chain breaks: 1 Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 918 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 897 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.32, per 1000 atoms: 0.66 Number of scatterers: 5045 At special positions: 0 Unit cell: (73.1, 63.64, 128.14, 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 24 16.00 O 970 8.00 N 872 7.00 C 3179 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS I 40 " - pdb=" SG CYS I 50 " distance=2.03 Simple disulfide: pdb=" SG CYS I 80 " - pdb=" SG CYS I 93 " distance=2.03 Simple disulfide: pdb=" SG CYS I 160 " - pdb=" SG CYS I 209 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN I 49 " Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 878.7 milliseconds 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1174 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 16 sheets defined 2.5% alpha, 34.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'I' and resid 98 through 100 No H-bonds generated for 'chain 'I' and resid 98 through 100' Processing helix chain 'I' and resid 127 through 129 No H-bonds generated for 'chain 'I' and resid 127 through 129' Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.567A pdb=" N PHE A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 removed outlier: 4.103A pdb=" N THR A 91 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 39 through 43 removed outlier: 3.799A pdb=" N GLN I 39 " --> pdb=" O THR I 51 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR I 47 " --> pdb=" O PHE I 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 78 through 79 removed outlier: 3.752A pdb=" N TYR I 67 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN I 109 " --> pdb=" O HIS I 66 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE I 106 " --> pdb=" O LEU I 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 136 through 141 removed outlier: 5.613A pdb=" N ASN I 137 " --> pdb=" O ASN I 153 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASN I 153 " --> pdb=" O ASN I 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 176 through 180 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 8 removed outlier: 3.945A pdb=" N THR H 69 " --> pdb=" O HIS H 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.513A pdb=" N VAL H 12 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU H 33 " --> pdb=" O ALA H 99 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.513A pdb=" N VAL H 12 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N CYS H 96 " --> pdb=" O TRP H 111 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TRP H 111 " --> pdb=" O CYS H 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 18 through 22 removed outlier: 3.718A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 34 through 38 removed outlier: 3.659A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.673A pdb=" N SER A 21 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.872A pdb=" N VAL A 12 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N MET A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLY A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.872A pdb=" N VAL A 12 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 4 through 5 Processing sheet with id=AB5, first strand: chain 'B' and resid 10 through 11 Processing sheet with id=AB6, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AB7, first strand: chain 'B' and resid 35 through 37 removed outlier: 6.533A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) 138 hydrogen bonds defined for protein. 339 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: 1.22 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1627 1.34 - 1.46: 1328 1.46 - 1.58: 2184 1.58 - 1.70: 0 1.70 - 1.81: 34 Bond restraints: 5173 Sorted by residual: bond pdb=" C5 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.15e+00 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.11e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.427 -0.021 2.00e-02 2.50e+03 1.07e+00 bond pdb=" CG1 ILE H 70 " pdb=" CD1 ILE H 70 " ideal model delta sigma weight residual 1.513 1.473 0.040 3.90e-02 6.57e+02 1.04e+00 bond pdb=" CB PRO L 8 " pdb=" CG PRO L 8 " ideal model delta sigma weight residual 1.492 1.543 -0.051 5.00e-02 4.00e+02 1.03e+00 ... (remaining 5168 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.42: 139 106.42 - 113.34: 2761 113.34 - 120.26: 1700 120.26 - 127.18: 2344 127.18 - 134.09: 74 Bond angle restraints: 7018 Sorted by residual: angle pdb=" CB LYS L 45 " pdb=" CG LYS L 45 " pdb=" CD LYS L 45 " ideal model delta sigma weight residual 111.30 118.72 -7.42 2.30e+00 1.89e-01 1.04e+01 angle pdb=" N SER L 52 " pdb=" CA SER L 52 " pdb=" C SER L 52 " ideal model delta sigma weight residual 114.62 111.13 3.49 1.14e+00 7.69e-01 9.38e+00 angle pdb=" C ILE H 48 " pdb=" N SER H 49 " pdb=" CA SER H 49 " ideal model delta sigma weight residual 121.75 116.65 5.10 1.73e+00 3.34e-01 8.70e+00 angle pdb=" C ASP H 109 " pdb=" N ILE H 110 " pdb=" CA ILE H 110 " ideal model delta sigma weight residual 121.97 127.21 -5.24 1.80e+00 3.09e-01 8.47e+00 angle pdb=" CA SER L 52 " pdb=" C SER L 52 " pdb=" N ASN L 53 " ideal model delta sigma weight residual 119.71 116.73 2.98 1.17e+00 7.31e-01 6.47e+00 ... (remaining 7013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.44: 2829 21.44 - 42.88: 207 42.88 - 64.33: 19 64.33 - 85.77: 16 85.77 - 107.21: 4 Dihedral angle restraints: 3075 sinusoidal: 1240 harmonic: 1835 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 168.78 -75.78 1 1.00e+01 1.00e-02 7.24e+01 dihedral pdb=" CA HIS I 141 " pdb=" C HIS I 141 " pdb=" N LYS I 142 " pdb=" CA LYS I 142 " ideal model delta harmonic sigma weight residual -180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CB CYS I 160 " pdb=" SG CYS I 160 " pdb=" SG CYS I 209 " pdb=" CB CYS I 209 " ideal model delta sinusoidal sigma weight residual -86.00 -53.76 -32.24 1 1.00e+01 1.00e-02 1.48e+01 ... (remaining 3072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 570 0.047 - 0.093: 136 0.093 - 0.140: 47 0.140 - 0.186: 3 0.186 - 0.233: 1 Chirality restraints: 757 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN I 49 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ILE H 51 " pdb=" N ILE H 51 " pdb=" C ILE H 51 " pdb=" CB ILE H 51 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ASN I 137 " pdb=" N ASN I 137 " pdb=" C ASN I 137 " pdb=" CB ASN I 137 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.40e-01 ... (remaining 754 not shown) Planarity restraints: 897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 7 " 0.050 5.00e-02 4.00e+02 7.45e-02 8.89e+00 pdb=" N PRO L 8 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN I 206 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO I 207 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO I 207 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO I 207 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 79 " -0.031 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO B 80 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 80 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 80 " -0.026 5.00e-02 4.00e+02 ... (remaining 894 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 360 2.73 - 3.27: 5009 3.27 - 3.81: 8017 3.81 - 4.36: 9185 4.36 - 4.90: 16263 Nonbonded interactions: 38834 Sorted by model distance: nonbonded pdb=" OG1 THR L 20 " pdb=" OG1 THR L 72 " model vdw 2.184 2.440 nonbonded pdb=" O PHE H 29 " pdb=" NH2 ARG H 72 " model vdw 2.189 2.520 nonbonded pdb=" OE2 GLU A 6 " pdb=" OG1 THR A 116 " model vdw 2.229 2.440 nonbonded pdb=" OD1 ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.238 2.440 nonbonded pdb=" OG SER H 52 " pdb=" OG1 THR H 56 " model vdw 2.240 2.440 ... (remaining 38829 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.230 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: 5.680 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.630 Find NCS groups from input model: 0.140 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 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 0.051 5173 Z= 0.254 Angle : 0.693 12.281 7018 Z= 0.359 Chirality : 0.046 0.233 757 Planarity : 0.005 0.075 896 Dihedral : 15.759 107.211 1880 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.28 % Favored : 90.40 % Rotamer: Outliers : 0.18 % Allowed : 1.08 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.32), residues: 625 helix: None (None), residues: 0 sheet: -0.53 (0.35), residues: 228 loop : -2.10 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 175 HIS 0.003 0.001 HIS A 95 PHE 0.012 0.002 PHE A 29 TYR 0.018 0.001 TYR H 50 ARG 0.003 0.000 ARG I 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: I 39 GLN cc_start: 0.7979 (mp10) cc_final: 0.7687 (mp10) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.1958 time to fit residues: 21.1447 Evaluate side-chains 74 residues out of total 558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 5.9990 chunk 46 optimal weight: 0.3980 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 31 optimal weight: 0.0980 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 HIS L 37 GLN A 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 5173 Z= 0.365 Angle : 0.754 12.320 7018 Z= 0.383 Chirality : 0.049 0.171 757 Planarity : 0.005 0.056 896 Dihedral : 8.072 56.258 735 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.92 % Favored : 89.76 % Rotamer: Outliers : 0.90 % Allowed : 12.01 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.33), residues: 625 helix: None (None), residues: 0 sheet: -0.91 (0.33), residues: 248 loop : -2.00 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 52 HIS 0.006 0.001 HIS A 95 PHE 0.014 0.002 PHE I 106 TYR 0.012 0.002 TYR A 111 ARG 0.003 0.001 ARG I 196 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 0.588 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 89 average time/residue: 0.2101 time to fit residues: 23.2716 Evaluate side-chains 81 residues out of total 558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 0.0000 chunk 18 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5173 Z= 0.195 Angle : 0.647 10.880 7018 Z= 0.328 Chirality : 0.046 0.210 757 Planarity : 0.005 0.050 896 Dihedral : 6.210 58.482 735 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.68 % Favored : 92.00 % Rotamer: Outliers : 1.25 % Allowed : 15.77 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.32), residues: 625 helix: None (None), residues: 0 sheet: -0.55 (0.35), residues: 227 loop : -2.03 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 52 HIS 0.004 0.001 HIS H 82 PHE 0.010 0.001 PHE H 29 TYR 0.014 0.001 TYR I 182 ARG 0.002 0.000 ARG I 196 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 94 average time/residue: 0.2010 time to fit residues: 23.6379 Evaluate side-chains 81 residues out of total 558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 33 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 82 HIS I 94 GLN I 96 GLN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5173 Z= 0.208 Angle : 0.648 11.161 7018 Z= 0.326 Chirality : 0.046 0.208 757 Planarity : 0.005 0.049 896 Dihedral : 5.842 57.763 735 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.28 % Favored : 90.40 % Rotamer: Outliers : 1.97 % Allowed : 18.64 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.32), residues: 625 helix: None (None), residues: 0 sheet: -0.48 (0.35), residues: 225 loop : -2.04 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 52 HIS 0.005 0.001 HIS I 141 PHE 0.009 0.001 PHE I 106 TYR 0.013 0.001 TYR I 182 ARG 0.009 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 142 LYS cc_start: 0.7626 (tttm) cc_final: 0.7311 (tptt) REVERT: B 38 GLN cc_start: 0.7678 (tp40) cc_final: 0.7113 (tp40) outliers start: 11 outliers final: 9 residues processed: 92 average time/residue: 0.1919 time to fit residues: 22.2648 Evaluate side-chains 92 residues out of total 558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 117 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 0.0040 chunk 24 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 5173 Z= 0.455 Angle : 0.810 13.775 7018 Z= 0.416 Chirality : 0.051 0.209 757 Planarity : 0.005 0.053 896 Dihedral : 6.681 52.722 735 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.52 % Favored : 88.16 % Rotamer: Outliers : 3.05 % Allowed : 20.97 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.32), residues: 625 helix: None (None), residues: 0 sheet: -0.99 (0.33), residues: 256 loop : -2.17 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 52 HIS 0.007 0.002 HIS I 141 PHE 0.014 0.002 PHE H 105 TYR 0.017 0.002 TYR A 94 ARG 0.006 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: I 142 LYS cc_start: 0.7620 (tttm) cc_final: 0.7385 (tttm) REVERT: A 117 LEU cc_start: 0.7463 (tt) cc_final: 0.7145 (tp) REVERT: B 38 GLN cc_start: 0.7750 (tp40) cc_final: 0.7205 (tp40) REVERT: B 97 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.8221 (p) outliers start: 17 outliers final: 14 residues processed: 95 average time/residue: 0.1911 time to fit residues: 22.9242 Evaluate side-chains 90 residues out of total 558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.0570 chunk 30 optimal weight: 9.9990 chunk 56 optimal weight: 0.0980 chunk 6 optimal weight: 0.9980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5173 Z= 0.173 Angle : 0.658 11.365 7018 Z= 0.330 Chirality : 0.046 0.215 757 Planarity : 0.005 0.054 896 Dihedral : 5.850 57.025 735 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.16 % Favored : 91.52 % Rotamer: Outliers : 2.69 % Allowed : 22.94 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.32), residues: 625 helix: None (None), residues: 0 sheet: -0.65 (0.34), residues: 230 loop : -2.04 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 52 HIS 0.003 0.001 HIS A 95 PHE 0.023 0.001 PHE I 156 TYR 0.013 0.001 TYR I 182 ARG 0.004 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 142 LYS cc_start: 0.7577 (tttm) cc_final: 0.7292 (tttp) REVERT: A 117 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6700 (tp) REVERT: B 38 GLN cc_start: 0.7735 (tp40) cc_final: 0.7497 (tp40) REVERT: B 97 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.8233 (p) outliers start: 15 outliers final: 10 residues processed: 104 average time/residue: 0.2119 time to fit residues: 27.1799 Evaluate side-chains 95 residues out of total 558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 35 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 0.0010 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 223 HIS ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5173 Z= 0.169 Angle : 0.660 11.778 7018 Z= 0.327 Chirality : 0.046 0.214 757 Planarity : 0.005 0.051 896 Dihedral : 5.522 55.175 735 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.00 % Favored : 91.68 % Rotamer: Outliers : 2.51 % Allowed : 25.63 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.32), residues: 625 helix: None (None), residues: 0 sheet: -0.47 (0.35), residues: 225 loop : -2.04 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 52 HIS 0.003 0.001 HIS I 141 PHE 0.019 0.001 PHE I 156 TYR 0.015 0.001 TYR I 182 ARG 0.006 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 142 LYS cc_start: 0.7527 (tttm) cc_final: 0.7217 (tttp) REVERT: B 38 GLN cc_start: 0.7730 (tp40) cc_final: 0.7452 (tp40) REVERT: B 97 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8267 (p) REVERT: B 106 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.6977 (tt) outliers start: 14 outliers final: 10 residues processed: 106 average time/residue: 0.2097 time to fit residues: 27.7688 Evaluate side-chains 98 residues out of total 558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 0.0970 chunk 46 optimal weight: 0.0970 chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5173 Z= 0.168 Angle : 0.665 11.517 7018 Z= 0.328 Chirality : 0.046 0.214 757 Planarity : 0.004 0.051 896 Dihedral : 5.402 55.141 735 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.36 % Favored : 92.32 % Rotamer: Outliers : 2.51 % Allowed : 25.81 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.32), residues: 625 helix: None (None), residues: 0 sheet: -0.45 (0.35), residues: 229 loop : -1.96 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 52 HIS 0.003 0.001 HIS H 82 PHE 0.014 0.001 PHE I 156 TYR 0.014 0.001 TYR I 182 ARG 0.003 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 142 LYS cc_start: 0.7467 (tttm) cc_final: 0.7224 (tttp) REVERT: A 34 MET cc_start: 0.8283 (mmm) cc_final: 0.7954 (mmm) REVERT: A 93 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7466 (tt) REVERT: B 38 GLN cc_start: 0.7673 (tp40) cc_final: 0.7410 (tp40) REVERT: B 97 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8282 (p) outliers start: 14 outliers final: 9 residues processed: 100 average time/residue: 0.1853 time to fit residues: 23.3814 Evaluate side-chains 95 residues out of total 558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5173 Z= 0.216 Angle : 0.695 11.992 7018 Z= 0.345 Chirality : 0.046 0.207 757 Planarity : 0.005 0.049 896 Dihedral : 5.612 57.797 735 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.80 % Favored : 90.88 % Rotamer: Outliers : 2.87 % Allowed : 25.81 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.33), residues: 625 helix: None (None), residues: 0 sheet: -0.53 (0.35), residues: 231 loop : -1.91 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 52 HIS 0.004 0.001 HIS A 95 PHE 0.013 0.001 PHE I 156 TYR 0.013 0.001 TYR I 182 ARG 0.008 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 142 LYS cc_start: 0.7465 (tttm) cc_final: 0.7265 (tttp) REVERT: A 34 MET cc_start: 0.8366 (mmm) cc_final: 0.7939 (mmm) REVERT: A 93 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7529 (tt) REVERT: B 97 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8284 (p) outliers start: 16 outliers final: 13 residues processed: 96 average time/residue: 0.1929 time to fit residues: 23.5171 Evaluate side-chains 98 residues out of total 558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5173 Z= 0.189 Angle : 0.685 9.231 7018 Z= 0.338 Chirality : 0.046 0.211 757 Planarity : 0.004 0.049 896 Dihedral : 5.497 56.287 735 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.68 % Favored : 92.00 % Rotamer: Outliers : 3.05 % Allowed : 25.99 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.33), residues: 625 helix: None (None), residues: 0 sheet: -0.51 (0.35), residues: 232 loop : -1.92 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 52 HIS 0.003 0.001 HIS A 95 PHE 0.012 0.001 PHE I 156 TYR 0.013 0.001 TYR I 182 ARG 0.008 0.000 ARG B 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 95 TYR cc_start: 0.7924 (m-80) cc_final: 0.7590 (m-80) REVERT: A 34 MET cc_start: 0.8349 (mmm) cc_final: 0.7966 (mmm) REVERT: A 39 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8461 (tp40) REVERT: A 93 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7500 (tt) REVERT: B 97 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8290 (p) outliers start: 17 outliers final: 13 residues processed: 103 average time/residue: 0.2162 time to fit residues: 27.8104 Evaluate side-chains 101 residues out of total 558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 2 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.098166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.086958 restraints weight = 15555.725| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.88 r_work: 0.3525 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5173 Z= 0.199 Angle : 0.692 9.168 7018 Z= 0.343 Chirality : 0.046 0.210 757 Planarity : 0.004 0.049 896 Dihedral : 5.534 56.708 735 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.00 % Favored : 91.68 % Rotamer: Outliers : 3.23 % Allowed : 25.63 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.33), residues: 625 helix: None (None), residues: 0 sheet: -0.54 (0.34), residues: 232 loop : -1.93 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 52 HIS 0.004 0.001 HIS I 141 PHE 0.012 0.001 PHE I 156 TYR 0.013 0.001 TYR I 182 ARG 0.003 0.000 ARG B 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1519.38 seconds wall clock time: 28 minutes 17.86 seconds (1697.86 seconds total)