Starting phenix.real_space_refine on Thu Jul 18 18:44:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly0_23581/07_2024/7ly0_23581.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly0_23581/07_2024/7ly0_23581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly0_23581/07_2024/7ly0_23581.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly0_23581/07_2024/7ly0_23581.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly0_23581/07_2024/7ly0_23581.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly0_23581/07_2024/7ly0_23581.cif" } resolution = 2.6 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= 0.039 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 10 5.16 5 C 1796 2.51 5 N 463 2.21 5 O 536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 82": "OE1" <-> "OE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 2805 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1033 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain breaks: 7 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "L" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 785 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 910 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" 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: 2.77, per 1000 atoms: 0.99 Number of scatterers: 2805 At special positions: 0 Unit cell: (73.5, 71.4, 74.55, 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 10 16.00 O 536 8.00 N 463 7.00 C 1796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " 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 ALPHA1-4 " NAG B 2 " - " MAN B 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " BETA1-6 " NAG B 1 " - " FUC B 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 149 " " NAG B 1 " - " ASN A 17 " Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 614.9 milliseconds 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 650 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 9 sheets defined 7.6% alpha, 47.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.185A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.544A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.445A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.349A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 95 Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.467A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.467A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.710A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.002A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) 103 hydrogen bonds defined for protein. 225 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: 0.77 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 520 1.32 - 1.45: 807 1.45 - 1.57: 1528 1.57 - 1.70: 4 1.70 - 1.82: 13 Bond restraints: 2872 Sorted by residual: bond pdb=" N TRP H 104 " pdb=" CA TRP H 104 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.16e-02 7.43e+03 8.17e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.468 -0.055 2.00e-02 2.50e+03 7.67e+00 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.37e+00 bond pdb=" CB ILE A 235 " pdb=" CG1 ILE A 235 " ideal model delta sigma weight residual 1.530 1.584 -0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" CG ASP A 138 " pdb=" OD1 ASP A 138 " ideal model delta sigma weight residual 1.249 1.198 0.051 1.90e-02 2.77e+03 7.23e+00 ... (remaining 2867 not shown) Histogram of bond angle deviations from ideal: 100.66 - 107.33: 91 107.33 - 114.01: 1571 114.01 - 120.69: 1210 120.69 - 127.36: 1006 127.36 - 134.04: 27 Bond angle restraints: 3905 Sorted by residual: angle pdb=" C GLN L 6 " pdb=" N PRO L 7 " pdb=" CA PRO L 7 " ideal model delta sigma weight residual 119.66 125.78 -6.12 7.30e-01 1.88e+00 7.02e+01 angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.03 127.32 -7.29 9.90e-01 1.02e+00 5.42e+01 angle pdb=" C ILE L 57 " pdb=" N PRO L 58 " pdb=" CA PRO L 58 " ideal model delta sigma weight residual 120.03 126.82 -6.79 9.90e-01 1.02e+00 4.71e+01 angle pdb=" C ARG L 53 " pdb=" N PRO L 54 " pdb=" CA PRO L 54 " ideal model delta sigma weight residual 119.92 127.22 -7.30 1.07e+00 8.73e-01 4.65e+01 angle pdb=" C PRO L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta sigma weight residual 119.19 126.17 -6.98 1.06e+00 8.90e-01 4.33e+01 ... (remaining 3900 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.83: 1668 17.83 - 35.65: 39 35.65 - 53.48: 14 53.48 - 71.30: 3 71.30 - 89.12: 1 Dihedral angle restraints: 1725 sinusoidal: 708 harmonic: 1017 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 51.87 41.13 1 1.00e+01 1.00e-02 2.37e+01 dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 87 " pdb=" CB CYS L 87 " ideal model delta sinusoidal sigma weight residual 93.00 55.35 37.65 1 1.00e+01 1.00e-02 2.00e+01 dihedral pdb=" CA ARG L 53 " pdb=" C ARG L 53 " pdb=" N PRO L 54 " pdb=" CA PRO L 54 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 1722 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.062: 296 0.062 - 0.124: 104 0.124 - 0.186: 29 0.186 - 0.248: 16 0.248 - 0.309: 5 Chirality restraints: 450 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.24e+01 chirality pdb=" C1 MAN B 3 " pdb=" O4 NAG B 2 " pdb=" C2 MAN B 3 " pdb=" O5 MAN B 3 " both_signs ideal model delta sigma weight residual False 2.40 2.47 -0.07 2.00e-02 2.50e+03 1.19e+01 chirality pdb=" C1 FUC B 4 " pdb=" O6 NAG B 1 " pdb=" C2 FUC B 4 " pdb=" O5 FUC B 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.82e+00 ... (remaining 447 not shown) Planarity restraints: 484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 33 " 0.035 2.00e-02 2.50e+03 1.89e-02 7.18e+00 pdb=" CG TYR L 33 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR L 33 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR L 33 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR L 33 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR L 33 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR L 33 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR L 33 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 122 " 0.024 2.00e-02 2.50e+03 2.31e-02 6.67e+00 pdb=" CG ASN A 122 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 122 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 122 " -0.033 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 103 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C GLU H 103 " 0.032 2.00e-02 2.50e+03 pdb=" O GLU H 103 " -0.012 2.00e-02 2.50e+03 pdb=" N TRP H 104 " -0.011 2.00e-02 2.50e+03 ... (remaining 481 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 1504 2.99 - 3.47: 2388 3.47 - 3.95: 4816 3.95 - 4.42: 5482 4.42 - 4.90: 8858 Nonbonded interactions: 23048 Sorted by model distance: nonbonded pdb=" NZ LYS A 77 " pdb=" O THR A 250 " model vdw 2.515 2.520 nonbonded pdb=" NZ LYS A 147 " pdb=" O LEU L 27 " model vdw 2.575 2.520 nonbonded pdb=" OD1 ASP L 91 " pdb=" N GLY L 94 " model vdw 2.576 2.520 nonbonded pdb=" OD1 ASP H 107 " pdb=" N TYR H 108 " model vdw 2.577 2.520 nonbonded pdb=" OG SER A 155 " pdb=" N GLU A 156 " model vdw 2.591 2.520 ... (remaining 23043 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: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.400 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 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 : 0.012 0.055 2872 Z= 0.771 Angle : 1.187 7.298 3905 Z= 0.800 Chirality : 0.080 0.309 450 Planarity : 0.005 0.019 481 Dihedral : 9.438 89.124 1066 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 0.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.36 % Allowed : 0.36 % Favored : 99.29 % 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: 1.70 (0.46), residues: 334 helix: None (None), residues: 0 sheet: 1.04 (0.39), residues: 154 loop : 1.42 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP L 34 HIS 0.002 0.001 HIS A 146 PHE 0.014 0.003 PHE A 175 TYR 0.035 0.004 TYR L 33 ARG 0.004 0.001 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.258 Fit side-chains REVERT: A 19 THR cc_start: 0.7681 (m) cc_final: 0.7459 (m) REVERT: A 86 PHE cc_start: 0.8153 (t80) cc_final: 0.7943 (t80) REVERT: L 20 ILE cc_start: 0.7448 (mt) cc_final: 0.7151 (mp) REVERT: L 31 TYR cc_start: 0.8175 (m-80) cc_final: 0.7627 (m-80) REVERT: L 53 ARG cc_start: 0.8227 (mtm110) cc_final: 0.7921 (mtm110) REVERT: L 86 TYR cc_start: 0.8811 (m-80) cc_final: 0.8570 (m-80) REVERT: L 98 VAL cc_start: 0.8630 (p) cc_final: 0.8395 (t) REVERT: H 18 LEU cc_start: 0.7209 (tt) cc_final: 0.7004 (tp) REVERT: H 27 PHE cc_start: 0.7322 (p90) cc_final: 0.6992 (p90) REVERT: H 45 LEU cc_start: 0.8886 (mt) cc_final: 0.8563 (mt) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.6697 time to fit residues: 67.5517 Evaluate side-chains 77 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 0.1980 chunk 25 optimal weight: 0.2980 chunk 14 optimal weight: 0.4980 chunk 8 optimal weight: 0.0970 chunk 17 optimal weight: 0.0980 chunk 13 optimal weight: 0.2980 chunk 26 optimal weight: 0.2980 chunk 10 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 0.0980 overall best weight: 0.1178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2872 Z= 0.177 Angle : 0.532 6.096 3905 Z= 0.276 Chirality : 0.043 0.163 450 Planarity : 0.004 0.034 481 Dihedral : 4.516 20.782 504 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.50 % Allowed : 11.79 % Favored : 85.71 % 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: 1.83 (0.47), residues: 334 helix: None (None), residues: 0 sheet: 1.19 (0.41), residues: 146 loop : 1.44 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 109 HIS 0.004 0.002 HIS A 245 PHE 0.008 0.001 PHE A 157 TYR 0.010 0.001 TYR H 95 ARG 0.004 0.001 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.285 Fit side-chains REVERT: A 86 PHE cc_start: 0.8309 (t80) cc_final: 0.8018 (t80) REVERT: A 190 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6369 (mtt-85) REVERT: A 248 TYR cc_start: 0.8292 (t80) cc_final: 0.8030 (t80) REVERT: L 20 ILE cc_start: 0.7588 (mt) cc_final: 0.7231 (mp) REVERT: L 31 TYR cc_start: 0.8240 (m-80) cc_final: 0.7705 (m-80) REVERT: L 51 SER cc_start: 0.7668 (OUTLIER) cc_final: 0.7387 (m) REVERT: H 16 ARG cc_start: 0.5975 (mtp180) cc_final: 0.5748 (mtm180) REVERT: H 27 PHE cc_start: 0.7351 (p90) cc_final: 0.7147 (p90) outliers start: 7 outliers final: 2 residues processed: 89 average time/residue: 0.6377 time to fit residues: 59.2117 Evaluate side-chains 82 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain L residue 51 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 25 optimal weight: 0.0980 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.1980 chunk 33 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 245 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 2872 Z= 0.358 Angle : 0.640 6.868 3905 Z= 0.331 Chirality : 0.047 0.170 450 Planarity : 0.005 0.047 481 Dihedral : 4.951 19.823 504 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.64 % Allowed : 13.57 % Favored : 81.79 % 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: 0.91 (0.46), residues: 334 helix: None (None), residues: 0 sheet: 0.62 (0.41), residues: 143 loop : 0.75 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.004 0.001 HIS A 245 PHE 0.015 0.002 PHE A 133 TYR 0.014 0.002 TYR L 31 ARG 0.004 0.001 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6414 (mtt-85) REVERT: A 248 TYR cc_start: 0.8523 (t80) cc_final: 0.8182 (t80) REVERT: L 9 SER cc_start: 0.5259 (p) cc_final: 0.4524 (t) REVERT: L 16 GLN cc_start: 0.5499 (mt0) cc_final: 0.4668 (mp10) REVERT: L 20 ILE cc_start: 0.7621 (mt) cc_final: 0.7197 (mp) REVERT: L 31 TYR cc_start: 0.8480 (m-80) cc_final: 0.7592 (m-80) REVERT: L 50 ASP cc_start: 0.8077 (m-30) cc_final: 0.7730 (m-30) REVERT: H 45 LEU cc_start: 0.8922 (mt) cc_final: 0.8679 (mt) outliers start: 13 outliers final: 9 residues processed: 95 average time/residue: 0.6989 time to fit residues: 69.1814 Evaluate side-chains 92 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain H residue 71 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 0.0670 chunk 14 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.0570 chunk 32 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 0.0000 chunk 0 optimal weight: 1.9990 overall best weight: 0.2440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2872 Z= 0.245 Angle : 0.548 5.691 3905 Z= 0.282 Chirality : 0.044 0.164 450 Planarity : 0.004 0.043 481 Dihedral : 4.630 17.376 504 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 5.00 % Allowed : 14.29 % Favored : 80.71 % 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: 0.75 (0.46), residues: 334 helix: None (None), residues: 0 sheet: 0.53 (0.41), residues: 146 loop : 0.63 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 47 HIS 0.003 0.001 HIS A 146 PHE 0.009 0.001 PHE A 133 TYR 0.010 0.001 TYR L 86 ARG 0.003 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6358 (mtt-85) REVERT: A 248 TYR cc_start: 0.8509 (t80) cc_final: 0.8185 (t80) REVERT: L 9 SER cc_start: 0.5189 (p) cc_final: 0.4525 (t) REVERT: L 16 GLN cc_start: 0.5509 (mt0) cc_final: 0.4688 (mp10) REVERT: L 20 ILE cc_start: 0.7687 (mt) cc_final: 0.7264 (mp) REVERT: L 31 TYR cc_start: 0.8499 (m-80) cc_final: 0.7681 (m-80) REVERT: H 45 LEU cc_start: 0.8911 (mt) cc_final: 0.8643 (mt) outliers start: 14 outliers final: 12 residues processed: 85 average time/residue: 0.8087 time to fit residues: 71.2533 Evaluate side-chains 87 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 71 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 0.0270 chunk 13 optimal weight: 0.0980 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 29 optimal weight: 0.3980 chunk 8 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 overall best weight: 0.1638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2872 Z= 0.188 Angle : 0.520 5.581 3905 Z= 0.267 Chirality : 0.043 0.158 450 Planarity : 0.004 0.040 481 Dihedral : 4.455 17.344 504 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 6.79 % Allowed : 13.93 % Favored : 79.29 % 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: 0.82 (0.47), residues: 334 helix: None (None), residues: 0 sheet: 0.58 (0.41), residues: 146 loop : 0.68 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 109 HIS 0.003 0.001 HIS H 35 PHE 0.008 0.001 PHE A 175 TYR 0.011 0.001 TYR L 31 ARG 0.002 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6331 (mtt-85) REVERT: A 248 TYR cc_start: 0.8499 (t80) cc_final: 0.8192 (t80) REVERT: L 9 SER cc_start: 0.4974 (p) cc_final: 0.4320 (t) REVERT: L 16 GLN cc_start: 0.5453 (mt0) cc_final: 0.4600 (mp10) REVERT: L 20 ILE cc_start: 0.7701 (mt) cc_final: 0.7273 (mp) REVERT: L 31 TYR cc_start: 0.8436 (m-80) cc_final: 0.7766 (m-80) REVERT: H 3 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.6781 (tm-30) outliers start: 19 outliers final: 11 residues processed: 84 average time/residue: 0.7219 time to fit residues: 62.7612 Evaluate side-chains 86 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 71 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 0.0870 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 0.0870 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 0.0170 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2872 Z= 0.275 Angle : 0.573 6.208 3905 Z= 0.290 Chirality : 0.045 0.158 450 Planarity : 0.004 0.042 481 Dihedral : 4.730 17.846 504 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 5.36 % Allowed : 16.07 % Favored : 78.57 % 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: 0.64 (0.47), residues: 334 helix: None (None), residues: 0 sheet: 0.41 (0.42), residues: 146 loop : 0.59 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.011 0.001 PHE A 175 TYR 0.011 0.001 TYR L 31 ARG 0.003 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6256 (mtt-85) REVERT: A 248 TYR cc_start: 0.8555 (t80) cc_final: 0.8251 (t80) REVERT: L 9 SER cc_start: 0.5176 (p) cc_final: 0.4492 (t) REVERT: L 16 GLN cc_start: 0.5285 (mt0) cc_final: 0.4640 (mp10) REVERT: L 20 ILE cc_start: 0.7710 (mt) cc_final: 0.7267 (mp) REVERT: L 31 TYR cc_start: 0.8356 (m-80) cc_final: 0.8116 (m-80) REVERT: H 3 GLN cc_start: 0.7165 (OUTLIER) cc_final: 0.6822 (tm-30) REVERT: H 45 LEU cc_start: 0.8836 (mt) cc_final: 0.8605 (mt) REVERT: H 80 TYR cc_start: 0.7126 (m-80) cc_final: 0.6559 (m-80) outliers start: 15 outliers final: 10 residues processed: 85 average time/residue: 0.7197 time to fit residues: 63.4882 Evaluate side-chains 88 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 71 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 18 optimal weight: 0.0070 chunk 27 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 15 optimal weight: 0.1980 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 overall best weight: 0.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2872 Z= 0.284 Angle : 0.575 6.393 3905 Z= 0.295 Chirality : 0.045 0.169 450 Planarity : 0.004 0.043 481 Dihedral : 4.807 17.408 504 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.64 % Allowed : 17.50 % Favored : 77.86 % 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 (0.46), residues: 334 helix: None (None), residues: 0 sheet: 0.44 (0.41), residues: 144 loop : 0.55 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.011 0.001 PHE A 133 TYR 0.010 0.001 TYR L 86 ARG 0.003 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.6719 (t0) cc_final: 0.6119 (m-40) REVERT: A 111 ASP cc_start: 0.7464 (p0) cc_final: 0.7046 (p0) REVERT: A 190 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6185 (mtt-85) REVERT: A 248 TYR cc_start: 0.8578 (t80) cc_final: 0.8250 (t80) REVERT: L 9 SER cc_start: 0.4931 (p) cc_final: 0.4248 (t) REVERT: L 16 GLN cc_start: 0.5394 (mt0) cc_final: 0.4704 (mp10) REVERT: L 20 ILE cc_start: 0.7723 (mt) cc_final: 0.7272 (mp) REVERT: L 31 TYR cc_start: 0.8377 (m-80) cc_final: 0.8041 (m-80) REVERT: H 3 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6849 (tm-30) REVERT: H 45 LEU cc_start: 0.8844 (mt) cc_final: 0.8604 (mt) REVERT: H 80 TYR cc_start: 0.7125 (m-80) cc_final: 0.6576 (m-80) outliers start: 13 outliers final: 9 residues processed: 84 average time/residue: 0.7587 time to fit residues: 66.0557 Evaluate side-chains 89 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 71 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 3 optimal weight: 0.0980 chunk 25 optimal weight: 0.2980 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 28 optimal weight: 0.4980 chunk 30 optimal weight: 0.0870 chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 0.0060 chunk 23 optimal weight: 0.3980 chunk 9 optimal weight: 0.3980 chunk 27 optimal weight: 0.1980 overall best weight: 0.1374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2872 Z= 0.170 Angle : 0.530 5.983 3905 Z= 0.271 Chirality : 0.044 0.166 450 Planarity : 0.004 0.039 481 Dihedral : 4.438 16.868 504 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.86 % Allowed : 18.93 % Favored : 78.21 % 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: 0.83 (0.47), residues: 334 helix: None (None), residues: 0 sheet: 0.72 (0.41), residues: 140 loop : 0.56 (0.48), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 109 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.001 PHE H 27 TYR 0.011 0.001 TYR L 86 ARG 0.002 0.000 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.6645 (t0) cc_final: 0.6094 (m-40) REVERT: A 113 LYS cc_start: 0.6314 (tppt) cc_final: 0.5068 (mmtt) REVERT: A 190 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.6121 (mtt-85) REVERT: A 248 TYR cc_start: 0.8537 (t80) cc_final: 0.8234 (t80) REVERT: L 9 SER cc_start: 0.5034 (p) cc_final: 0.4390 (t) REVERT: L 16 GLN cc_start: 0.5302 (mt0) cc_final: 0.4688 (mp10) REVERT: L 20 ILE cc_start: 0.7720 (mt) cc_final: 0.7275 (mp) REVERT: L 31 TYR cc_start: 0.8383 (m-80) cc_final: 0.7978 (m-80) REVERT: H 3 GLN cc_start: 0.7089 (OUTLIER) cc_final: 0.6849 (tm-30) REVERT: H 38 ARG cc_start: 0.8542 (ptt180) cc_final: 0.8059 (ptt180) REVERT: H 80 TYR cc_start: 0.7073 (m-80) cc_final: 0.6542 (m-80) outliers start: 8 outliers final: 5 residues processed: 80 average time/residue: 0.7759 time to fit residues: 64.3024 Evaluate side-chains 82 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 5 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 0.9990 chunk 30 optimal weight: 0.0770 chunk 20 optimal weight: 0.0670 chunk 32 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.1980 chunk 31 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 overall best weight: 0.2676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2872 Z= 0.264 Angle : 0.579 6.088 3905 Z= 0.294 Chirality : 0.045 0.187 450 Planarity : 0.004 0.042 481 Dihedral : 4.711 17.667 504 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.21 % Allowed : 19.64 % Favored : 77.14 % 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: 0.60 (0.46), residues: 334 helix: None (None), residues: 0 sheet: 0.41 (0.40), residues: 145 loop : 0.55 (0.49), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 47 HIS 0.004 0.001 HIS A 146 PHE 0.011 0.001 PHE H 27 TYR 0.009 0.001 TYR H 95 ARG 0.003 0.000 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.6702 (t0) cc_final: 0.6178 (m-40) REVERT: A 111 ASP cc_start: 0.7446 (p0) cc_final: 0.7019 (p0) REVERT: A 190 ARG cc_start: 0.6913 (OUTLIER) cc_final: 0.6156 (mtt-85) REVERT: A 248 TYR cc_start: 0.8559 (t80) cc_final: 0.8230 (t80) REVERT: L 9 SER cc_start: 0.4900 (p) cc_final: 0.4220 (t) REVERT: L 16 GLN cc_start: 0.5382 (mt0) cc_final: 0.4701 (mp10) REVERT: L 20 ILE cc_start: 0.7731 (mt) cc_final: 0.7282 (mp) REVERT: L 31 TYR cc_start: 0.8407 (m-80) cc_final: 0.8007 (m-80) REVERT: H 3 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6892 (tm-30) REVERT: H 43 LYS cc_start: 0.7766 (mmtt) cc_final: 0.7556 (mmtt) REVERT: H 45 LEU cc_start: 0.8859 (mt) cc_final: 0.8629 (mt) REVERT: H 80 TYR cc_start: 0.7032 (m-80) cc_final: 0.6543 (m-80) outliers start: 9 outliers final: 7 residues processed: 79 average time/residue: 0.7965 time to fit residues: 65.1888 Evaluate side-chains 85 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 5 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 0.0040 chunk 24 optimal weight: 0.0030 chunk 3 optimal weight: 0.0870 chunk 7 optimal weight: 0.3980 chunk 27 optimal weight: 0.1980 chunk 11 optimal weight: 0.0980 chunk 4 optimal weight: 0.6980 overall best weight: 0.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 2872 Z= 0.145 Angle : 0.513 6.255 3905 Z= 0.265 Chirality : 0.044 0.165 450 Planarity : 0.004 0.038 481 Dihedral : 4.267 16.647 504 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.21 % Allowed : 19.29 % Favored : 77.50 % 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: 0.70 (0.47), residues: 334 helix: None (None), residues: 0 sheet: 0.46 (0.40), residues: 156 loop : 0.64 (0.51), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.010 0.001 PHE H 27 TYR 0.011 0.001 TYR L 86 ARG 0.002 0.000 ARG A 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.6567 (t0) cc_final: 0.6168 (m-40) REVERT: A 113 LYS cc_start: 0.6310 (tppt) cc_final: 0.5072 (mmtt) REVERT: A 248 TYR cc_start: 0.8504 (t80) cc_final: 0.8212 (t80) REVERT: L 16 GLN cc_start: 0.5299 (mt0) cc_final: 0.4710 (mp10) REVERT: L 20 ILE cc_start: 0.7724 (mt) cc_final: 0.7285 (mp) REVERT: L 31 TYR cc_start: 0.8393 (m-80) cc_final: 0.7942 (m-80) REVERT: H 80 TYR cc_start: 0.7030 (m-80) cc_final: 0.6493 (m-80) outliers start: 9 outliers final: 5 residues processed: 82 average time/residue: 0.7704 time to fit residues: 65.4721 Evaluate side-chains 78 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain H residue 5 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 23 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 0.0870 chunk 12 optimal weight: 0.0970 chunk 33 optimal weight: 0.0040 overall best weight: 0.1968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.187900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.182123 restraints weight = 2964.066| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 0.75 r_work: 0.3917 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.3849 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2872 Z= 0.214 Angle : 0.553 6.055 3905 Z= 0.281 Chirality : 0.044 0.173 450 Planarity : 0.004 0.040 481 Dihedral : 4.426 17.493 504 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.14 % Allowed : 20.71 % Favored : 77.14 % 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: 0.79 (0.47), residues: 334 helix: None (None), residues: 0 sheet: 0.66 (0.41), residues: 142 loop : 0.56 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 109 HIS 0.002 0.001 HIS H 35 PHE 0.009 0.001 PHE H 27 TYR 0.011 0.001 TYR H 53 ARG 0.002 0.000 ARG H 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1930.68 seconds wall clock time: 37 minutes 6.07 seconds (2226.07 seconds total)