Starting phenix.real_space_refine on Wed Mar 5 17:06:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ly0_23581/03_2025/7ly0_23581.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ly0_23581/03_2025/7ly0_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/cci-nas-00/data/ceres_data/7ly0_23581/03_2025/7ly0_23581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ly0_23581/03_2025/7ly0_23581.map" model { file = "/net/cci-nas-00/data/ceres_data/7ly0_23581/03_2025/7ly0_23581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ly0_23581/03_2025/7ly0_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. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.57, per 1000 atoms: 1.27 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 0.81 Conformation dependent library (CDL) restraints added in 325.1 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: 0.40 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: 0.70 Time building geometry restraints manager: 0.93 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: 0.00 - 1.46: 3280 1.46 - 2.92: 518 2.92 - 4.38: 68 4.38 - 5.84: 25 5.84 - 7.30: 14 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 3.120 nonbonded pdb=" NZ LYS A 147 " pdb=" O LEU L 27 " model vdw 2.575 3.120 nonbonded pdb=" OD1 ASP L 91 " pdb=" N GLY L 94 " model vdw 2.576 3.120 nonbonded pdb=" OD1 ASP H 107 " pdb=" N TYR H 108 " model vdw 2.577 3.120 nonbonded pdb=" OG SER A 155 " pdb=" N GLU A 156 " model vdw 2.591 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 3.590 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.640 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:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.300 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.301 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: 0.7265 time to fit residues: 73.1858 Evaluate side-chains 77 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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: 0.2980 chunk 25 optimal weight: 0.2980 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 0.1980 chunk 17 optimal weight: 0.4980 chunk 13 optimal weight: 0.0770 chunk 26 optimal weight: 0.0970 chunk 10 optimal weight: 0.0670 chunk 16 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 overall best weight: 0.1474 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.190209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.184937 restraints weight = 2807.619| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 0.67 r_work: 0.3937 rms_B_bonded: 0.87 restraints_weight: 0.5000 r_work: 0.3870 rms_B_bonded: 1.72 restraints_weight: 0.2500 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2872 Z= 0.201 Angle : 0.555 5.959 3905 Z= 0.287 Chirality : 0.044 0.158 450 Planarity : 0.004 0.034 481 Dihedral : 4.546 21.060 504 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.95 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: 1.74 (0.46), residues: 334 helix: None (None), residues: 0 sheet: 1.17 (0.41), residues: 146 loop : 1.35 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 34 HIS 0.004 0.001 HIS A 245 PHE 0.009 0.001 PHE A 157 TYR 0.008 0.001 TYR H 95 ARG 0.004 0.000 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 93 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.311 Fit side-chains REVERT: A 19 THR cc_start: 0.8063 (m) cc_final: 0.7754 (m) REVERT: A 86 PHE cc_start: 0.8366 (t80) cc_final: 0.8159 (t80) REVERT: A 190 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6829 (mtt-85) REVERT: L 31 TYR cc_start: 0.8332 (m-80) cc_final: 0.8030 (m-80) REVERT: H 45 LEU cc_start: 0.8752 (mt) cc_final: 0.8490 (mt) outliers start: 7 outliers final: 3 residues processed: 88 average time/residue: 0.6872 time to fit residues: 62.9791 Evaluate side-chains 79 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 188 ASN Chi-restraints excluded: chain A residue 190 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 18 optimal weight: 0.0270 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 0.0470 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 0.2980 chunk 1 optimal weight: 0.0980 chunk 29 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 overall best weight: 0.1536 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.186407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.181178 restraints weight = 2814.696| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 0.66 r_work: 0.3883 rms_B_bonded: 0.97 restraints_weight: 0.5000 r_work: 0.3810 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2872 Z= 0.201 Angle : 0.529 5.479 3905 Z= 0.278 Chirality : 0.043 0.159 450 Planarity : 0.004 0.038 481 Dihedral : 4.395 21.234 504 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.21 % Allowed : 15.00 % 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: 1.49 (0.47), residues: 334 helix: None (None), residues: 0 sheet: 0.96 (0.40), residues: 154 loop : 1.22 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 34 HIS 0.003 0.001 HIS H 35 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 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 90 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.321 Fit side-chains REVERT: A 19 THR cc_start: 0.8104 (m) cc_final: 0.7831 (m) REVERT: A 104 TRP cc_start: 0.8649 (m-90) cc_final: 0.8435 (m-90) REVERT: A 190 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6879 (mtt-85) REVERT: L 31 TYR cc_start: 0.8440 (m-80) cc_final: 0.7988 (m-80) outliers start: 9 outliers final: 3 residues processed: 84 average time/residue: 0.6950 time to fit residues: 60.9557 Evaluate side-chains 76 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 191 GLU 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 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 16 optimal weight: 0.0970 chunk 25 optimal weight: 0.2980 chunk 8 optimal weight: 0.4980 chunk 23 optimal weight: 0.0010 chunk 33 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 overall best weight: 0.3184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.181727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.176118 restraints weight = 2837.150| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 0.68 r_work: 0.3827 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 2872 Z= 0.319 Angle : 0.603 6.279 3905 Z= 0.312 Chirality : 0.046 0.159 450 Planarity : 0.005 0.043 481 Dihedral : 4.849 20.114 504 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 5.00 % Allowed : 15.00 % Favored : 80.00 % 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 (0.46), residues: 334 helix: None (None), residues: 0 sheet: 0.46 (0.42), residues: 146 loop : 0.55 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 52 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE A 175 TYR 0.012 0.002 TYR L 31 ARG 0.004 0.001 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 91 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.290 Fit side-chains REVERT: A 190 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.6934 (mtt-85) REVERT: A 248 TYR cc_start: 0.8226 (t80) cc_final: 0.8004 (t80) REVERT: L 9 SER cc_start: 0.5468 (p) cc_final: 0.4868 (t) REVERT: L 31 TYR cc_start: 0.8572 (m-80) cc_final: 0.7836 (m-80) REVERT: H 27 PHE cc_start: 0.7526 (p90) cc_final: 0.7305 (p90) outliers start: 14 outliers final: 9 residues processed: 84 average time/residue: 0.8737 time to fit residues: 75.9711 Evaluate side-chains 80 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 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 68 THR Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 96 SER 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 18 optimal weight: 0.9990 chunk 24 optimal weight: 0.0570 chunk 21 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 0.0980 chunk 30 optimal weight: 0.7980 overall best weight: 0.4098 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.178057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.172579 restraints weight = 2808.290| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 0.67 r_work: 0.3773 rms_B_bonded: 0.97 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 2872 Z= 0.383 Angle : 0.641 6.698 3905 Z= 0.328 Chirality : 0.048 0.177 450 Planarity : 0.005 0.045 481 Dihedral : 5.076 19.191 504 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.71 % Allowed : 16.07 % 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: 0.09 (0.46), residues: 334 helix: None (None), residues: 0 sheet: 0.05 (0.41), residues: 147 loop : 0.21 (0.47), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 52 HIS 0.004 0.002 HIS A 245 PHE 0.014 0.002 PHE A 133 TYR 0.016 0.002 TYR L 31 ARG 0.003 0.001 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 94 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.339 Fit side-chains REVERT: A 190 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.6899 (mtt-85) REVERT: A 248 TYR cc_start: 0.8302 (t80) cc_final: 0.8036 (t80) REVERT: L 31 TYR cc_start: 0.8451 (m-80) cc_final: 0.8207 (m-80) REVERT: H 27 PHE cc_start: 0.7547 (p90) cc_final: 0.7342 (p90) REVERT: H 80 TYR cc_start: 0.7276 (m-80) cc_final: 0.6878 (m-80) outliers start: 16 outliers final: 9 residues processed: 84 average time/residue: 0.7945 time to fit residues: 69.1794 Evaluate side-chains 85 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 190 ARG Chi-restraints excluded: chain A residue 191 GLU 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 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 19 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 13 optimal weight: 0.0050 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 16 optimal weight: 0.0270 chunk 24 optimal weight: 0.3980 chunk 1 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 overall best weight: 0.3452 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.180466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.174912 restraints weight = 2826.621| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 0.69 r_work: 0.3838 rms_B_bonded: 0.86 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 1.69 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 2872 Z= 0.334 Angle : 0.616 6.144 3905 Z= 0.315 Chirality : 0.047 0.170 450 Planarity : 0.005 0.045 481 Dihedral : 5.062 18.589 504 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.71 % Allowed : 17.14 % 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: 0.04 (0.46), residues: 334 helix: None (None), residues: 0 sheet: 0.07 (0.41), residues: 146 loop : 0.13 (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 0.014 0.001 PHE A 133 TYR 0.011 0.002 TYR L 33 ARG 0.002 0.001 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 91 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.328 Fit side-chains REVERT: A 99 ASN cc_start: 0.6966 (t0) cc_final: 0.6709 (m-40) REVERT: A 157 PHE cc_start: 0.8049 (m-80) cc_final: 0.7821 (m-80) REVERT: A 248 TYR cc_start: 0.8335 (t80) cc_final: 0.8085 (t80) REVERT: L 31 TYR cc_start: 0.8559 (m-80) cc_final: 0.8127 (m-80) REVERT: H 27 PHE cc_start: 0.7598 (p90) cc_final: 0.7389 (p90) REVERT: H 80 TYR cc_start: 0.7270 (m-80) cc_final: 0.6824 (m-80) outliers start: 16 outliers final: 11 residues processed: 82 average time/residue: 0.8606 time to fit residues: 73.0037 Evaluate side-chains 84 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 162 SER Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain L residue 65 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 0.0970 chunk 17 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 chunk 23 optimal weight: 0.0980 chunk 12 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.180013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.174407 restraints weight = 2852.215| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 0.68 r_work: 0.3831 rms_B_bonded: 0.87 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 1.65 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 2872 Z= 0.341 Angle : 0.625 6.432 3905 Z= 0.321 Chirality : 0.047 0.192 450 Planarity : 0.005 0.045 481 Dihedral : 5.165 18.777 504 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.64 % Allowed : 18.93 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.46), residues: 334 helix: None (None), residues: 0 sheet: -0.07 (0.40), residues: 148 loop : 0.03 (0.49), residues: 186 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 0.014 0.001 PHE A 133 TYR 0.011 0.002 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 89 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.279 Fit side-chains REVERT: A 99 ASN cc_start: 0.7006 (t0) cc_final: 0.6748 (m-40) REVERT: A 248 TYR cc_start: 0.8338 (t80) cc_final: 0.8093 (t80) REVERT: L 31 TYR cc_start: 0.8585 (m-80) cc_final: 0.7979 (m-80) REVERT: H 80 TYR cc_start: 0.7273 (m-80) cc_final: 0.6844 (m-80) outliers start: 13 outliers final: 10 residues processed: 80 average time/residue: 0.7848 time to fit residues: 65.0844 Evaluate side-chains 84 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 162 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain L residue 65 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 13 optimal weight: 0.0970 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 25 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 0.0980 chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 overall best weight: 0.2978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.180737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.175229 restraints weight = 2811.886| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 0.68 r_work: 0.3838 rms_B_bonded: 0.87 restraints_weight: 0.5000 r_work: 0.3772 rms_B_bonded: 1.69 restraints_weight: 0.2500 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2872 Z= 0.296 Angle : 0.611 6.164 3905 Z= 0.313 Chirality : 0.047 0.187 450 Planarity : 0.005 0.043 481 Dihedral : 5.060 18.561 504 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 5.00 % Allowed : 18.57 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.46), residues: 334 helix: None (None), residues: 0 sheet: 0.16 (0.42), residues: 134 loop : 0.02 (0.47), residues: 200 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 0.014 0.001 PHE A 133 TYR 0.012 0.002 TYR L 31 ARG 0.002 0.000 ARG A 246 *********************** 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 91 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.294 Fit side-chains REVERT: A 99 ASN cc_start: 0.6973 (t0) cc_final: 0.6730 (m-40) REVERT: A 248 TYR cc_start: 0.8337 (t80) cc_final: 0.8095 (t80) REVERT: H 80 TYR cc_start: 0.7266 (m-80) cc_final: 0.6898 (m-80) outliers start: 14 outliers final: 12 residues processed: 82 average time/residue: 0.7405 time to fit residues: 63.0434 Evaluate side-chains 86 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 162 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain L residue 65 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.0980 chunk 17 optimal weight: 0.1980 chunk 31 optimal weight: 0.8980 chunk 9 optimal weight: 0.1980 chunk 20 optimal weight: 0.5980 chunk 6 optimal weight: 0.2980 chunk 11 optimal weight: 0.3980 chunk 13 optimal weight: 0.4980 chunk 15 optimal weight: 0.2980 chunk 24 optimal weight: 0.0980 overall best weight: 0.1780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.182815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.177333 restraints weight = 2780.922| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 0.67 r_work: 0.3863 rms_B_bonded: 0.88 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 1.69 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3788 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= 0.206 Angle : 0.564 5.367 3905 Z= 0.292 Chirality : 0.045 0.182 450 Planarity : 0.004 0.042 481 Dihedral : 4.761 18.708 504 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.57 % Allowed : 20.00 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.47), residues: 334 helix: None (None), residues: 0 sheet: 0.17 (0.42), residues: 136 loop : 0.21 (0.48), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 152 HIS 0.002 0.001 HIS H 35 PHE 0.015 0.001 PHE H 27 TYR 0.010 0.001 TYR L 86 ARG 0.002 0.000 ARG A 246 *********************** 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 84 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.312 Fit side-chains REVERT: A 99 ASN cc_start: 0.6930 (t0) cc_final: 0.6382 (m-40) REVERT: A 248 TYR cc_start: 0.8284 (t80) cc_final: 0.8031 (t80) REVERT: L 31 TYR cc_start: 0.8471 (m-80) cc_final: 0.8082 (m-10) REVERT: H 80 TYR cc_start: 0.7208 (m-80) cc_final: 0.6828 (m-80) outliers start: 10 outliers final: 8 residues processed: 78 average time/residue: 0.7587 time to fit residues: 61.5208 Evaluate side-chains 79 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 162 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 96 SER 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 18 optimal weight: 0.0470 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.0980 chunk 31 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 0.0970 chunk 5 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 overall best weight: 0.1676 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.187539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.181692 restraints weight = 2994.484| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 0.75 r_work: 0.3907 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.3835 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2872 Z= 0.203 Angle : 0.569 5.349 3905 Z= 0.294 Chirality : 0.045 0.181 450 Planarity : 0.004 0.042 481 Dihedral : 4.653 19.017 504 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.86 % Allowed : 21.07 % Favored : 76.07 % 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: 0.27 (0.47), residues: 334 helix: None (None), residues: 0 sheet: 0.36 (0.42), residues: 134 loop : 0.16 (0.48), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.003 0.001 HIS A 146 PHE 0.009 0.001 PHE A 133 TYR 0.012 0.001 TYR L 33 ARG 0.002 0.000 ARG H 72 ********************** 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 76 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.312 Fit side-chains REVERT: A 99 ASN cc_start: 0.7015 (t0) cc_final: 0.6419 (m-40) REVERT: A 248 TYR cc_start: 0.8287 (t80) cc_final: 0.8037 (t80) REVERT: L 31 TYR cc_start: 0.8467 (m-80) cc_final: 0.8151 (m-10) REVERT: H 43 LYS cc_start: 0.8119 (mmtt) cc_final: 0.7793 (mmtm) REVERT: H 80 TYR cc_start: 0.7225 (m-80) cc_final: 0.6866 (m-80) outliers start: 8 outliers final: 8 residues processed: 73 average time/residue: 0.6938 time to fit residues: 52.8024 Evaluate side-chains 76 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 96 SER 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 24 optimal weight: 0.0870 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 0 optimal weight: 0.2980 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 0.0870 chunk 7 optimal weight: 0.6980 chunk 17 optimal weight: 0.0980 chunk 19 optimal weight: 0.4980 overall best weight: 0.1336 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.188311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.182617 restraints weight = 2936.601| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 0.73 r_work: 0.3917 rms_B_bonded: 1.04 restraints_weight: 0.5000 r_work: 0.3846 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2872 Z= 0.176 Angle : 0.550 5.089 3905 Z= 0.285 Chirality : 0.045 0.173 450 Planarity : 0.004 0.041 481 Dihedral : 4.529 18.875 504 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.57 % Allowed : 21.43 % Favored : 75.00 % 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: 0.34 (0.47), residues: 334 helix: None (None), residues: 0 sheet: 0.48 (0.42), residues: 135 loop : 0.14 (0.48), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 152 HIS 0.002 0.001 HIS H 35 PHE 0.008 0.001 PHE A 133 TYR 0.011 0.001 TYR L 33 ARG 0.001 0.000 ARG H 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2895.06 seconds wall clock time: 50 minutes 5.19 seconds (3005.19 seconds total)