Starting phenix.real_space_refine on Thu Jul 24 11:44:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jva_36672/07_2025/8jva_36672.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jva_36672/07_2025/8jva_36672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jva_36672/07_2025/8jva_36672.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jva_36672/07_2025/8jva_36672.map" model { file = "/net/cci-nas-00/data/ceres_data/8jva_36672/07_2025/8jva_36672.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jva_36672/07_2025/8jva_36672.cif" } resolution = 2.81 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= -0.002 sd= 0.015 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 20 5.16 5 C 3862 2.51 5 N 1002 2.21 5 O 1187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6071 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "A" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1652 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain: "B" Number of atoms: 1455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1455 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 1 Chain: "F" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1972 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 15, 'TRANS': 227} Chain breaks: 6 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.01, per 1000 atoms: 0.99 Number of scatterers: 6071 At special positions: 0 Unit cell: (76.68, 73.44, 147.96, 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 20 16.00 O 1187 8.00 N 1002 7.00 C 3862 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " 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 NAG-ASN " NAG F 401 " - " ASN F 122 " " NAG F 402 " - " ASN F 165 " " NAG F 403 " - " ASN F 282 " " NAG F 404 " - " ASN F 234 " " NAG F 405 " - " ASN F 61 " Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 939.9 milliseconds 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 16 sheets defined 5.9% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 61 through 65 removed outlier: 3.929A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.676A pdb=" N THR D 91 " --> pdb=" O PRO D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 103 removed outlier: 4.016A pdb=" N GLN D 103 " --> pdb=" O PRO D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 100 through 103' Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.904A pdb=" N SER B 31 " --> pdb=" O THR B 28 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.689A pdb=" N THR B 90 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 303 removed outlier: 3.635A pdb=" N LYS F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.548A pdb=" N ASN D 97 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ARG D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.613A pdb=" N ASP A 70 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 10 through 13 Processing sheet with id=AA5, first strand: chain 'A' and resid 45 through 49 removed outlier: 6.665A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N SER A 49 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU A 33 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 114 through 118 removed outlier: 3.935A pdb=" N ASN A 137 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 145 through 150 removed outlier: 4.066A pdb=" N TYR A 192 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.177A pdb=" N GLY B 10 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N MET B 34 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG B 52 " --> pdb=" O ASN B 56 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASN B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.177A pdb=" N GLY B 10 " --> pdb=" O THR B 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 128 through 129 removed outlier: 3.821A pdb=" N VAL B 152 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 27 through 30 removed outlier: 4.097A pdb=" N ALA F 27 " --> pdb=" O TRP F 64 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR F 63 " --> pdb=" O VAL F 267 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL F 227 " --> pdb=" O ILE F 203 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N SER F 205 " --> pdb=" O PRO F 225 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 47 through 55 removed outlier: 3.561A pdb=" N VAL F 47 " --> pdb=" O TYR F 279 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP F 287 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.994A pdb=" N SER F 162 " --> pdb=" O GLN F 134 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.547A pdb=" N SER F 172 " --> pdb=" O VAL F 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 141 through 145 removed outlier: 5.924A pdb=" N LEU F 141 " --> pdb=" O LEU F 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 215 hydrogen bonds defined for protein. 531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1923 1.34 - 1.46: 1599 1.46 - 1.58: 2671 1.58 - 1.70: 0 1.70 - 1.82: 26 Bond restraints: 6219 Sorted by residual: bond pdb=" C1 NAG F 402 " pdb=" O5 NAG F 402 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C1 NAG F 405 " pdb=" O5 NAG F 405 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.11e+00 bond pdb=" C1 NAG F 403 " pdb=" O5 NAG F 403 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.97e+00 bond pdb=" C5 NAG F 405 " pdb=" O5 NAG F 405 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.33e+00 bond pdb=" C5 NAG F 403 " pdb=" O5 NAG F 403 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.20e+00 ... (remaining 6214 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 8234 1.69 - 3.37: 193 3.37 - 5.06: 21 5.06 - 6.75: 3 6.75 - 8.44: 1 Bond angle restraints: 8452 Sorted by residual: angle pdb=" N ILE F 100 " pdb=" CA ILE F 100 " pdb=" C ILE F 100 " ideal model delta sigma weight residual 112.96 108.70 4.26 1.00e+00 1.00e+00 1.81e+01 angle pdb=" C TYR B 103 " pdb=" CA TYR B 103 " pdb=" CB TYR B 103 " ideal model delta sigma weight residual 117.23 111.53 5.70 1.36e+00 5.41e-01 1.76e+01 angle pdb=" C PHE F 32 " pdb=" CA PHE F 32 " pdb=" CB PHE F 32 " ideal model delta sigma weight residual 115.89 110.98 4.91 1.32e+00 5.74e-01 1.38e+01 angle pdb=" N GLY B 149 " pdb=" CA GLY B 149 " pdb=" C GLY B 149 " ideal model delta sigma weight residual 110.87 115.91 -5.04 1.54e+00 4.22e-01 1.07e+01 angle pdb=" CA GLY A 66 " pdb=" C GLY A 66 " pdb=" O GLY A 66 " ideal model delta sigma weight residual 122.45 120.16 2.29 7.20e-01 1.93e+00 1.01e+01 ... (remaining 8447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 3391 16.77 - 33.54: 290 33.54 - 50.32: 53 50.32 - 67.09: 8 67.09 - 83.86: 4 Dihedral angle restraints: 3746 sinusoidal: 1516 harmonic: 2230 Sorted by residual: dihedral pdb=" CB CYS A 134 " pdb=" SG CYS A 134 " pdb=" SG CYS A 194 " pdb=" CB CYS A 194 " ideal model delta sinusoidal sigma weight residual 93.00 169.35 -76.35 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 134.15 -41.15 1 1.00e+01 1.00e-02 2.37e+01 dihedral pdb=" CA ASP A 167 " pdb=" C ASP A 167 " pdb=" N SER A 168 " pdb=" CA SER A 168 " ideal model delta harmonic sigma weight residual -180.00 -162.52 -17.48 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 3743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 627 0.036 - 0.071: 207 0.071 - 0.107: 78 0.107 - 0.142: 32 0.142 - 0.178: 2 Chirality restraints: 946 Sorted by residual: chirality pdb=" C1 NAG F 403 " pdb=" ND2 ASN F 282 " pdb=" C2 NAG F 403 " pdb=" O5 NAG F 403 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.92e-01 chirality pdb=" CA GLU B 158 " pdb=" N GLU B 158 " pdb=" C GLU B 158 " pdb=" CB GLU B 158 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" C1 NAG F 402 " pdb=" ND2 ASN F 165 " pdb=" C2 NAG F 402 " pdb=" O5 NAG F 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 943 not shown) Planarity restraints: 1085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 53 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.40e+00 pdb=" N PRO D 54 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 54 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 54 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 126 " -0.034 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO B 127 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 127 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 127 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 58 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO A 59 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 59 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 59 " 0.024 5.00e-02 4.00e+02 ... (remaining 1082 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 700 2.75 - 3.29: 5199 3.29 - 3.83: 8847 3.83 - 4.36: 10352 4.36 - 4.90: 19171 Nonbonded interactions: 44269 Sorted by model distance: nonbonded pdb=" OG SER F 94 " pdb=" OE1 GLU F 96 " model vdw 2.217 3.040 nonbonded pdb=" OG SER D 35 " pdb=" O ALA D 49 " model vdw 2.251 3.040 nonbonded pdb=" OD2 ASP F 40 " pdb=" NH2 ARG F 44 " model vdw 2.304 3.120 nonbonded pdb=" O ARG B 52 " pdb=" NH1 ARG B 71 " model vdw 2.310 3.120 nonbonded pdb=" O SER A 114 " pdb=" OG SER A 114 " model vdw 2.321 3.040 ... (remaining 44264 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: 55.800 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.050 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6230 Z= 0.172 Angle : 0.636 8.436 8479 Z= 0.350 Chirality : 0.044 0.178 946 Planarity : 0.005 0.063 1080 Dihedral : 12.608 83.859 2298 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.47 (0.30), residues: 747 helix: 0.33 (1.21), residues: 16 sheet: 0.87 (0.32), residues: 283 loop : -1.18 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.016 0.001 PHE F 220 TYR 0.016 0.001 TYR A 140 ARG 0.003 0.000 ARG D 31 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 5) link_NAG-ASN : angle 2.03959 ( 15) hydrogen bonds : bond 0.16763 ( 195) hydrogen bonds : angle 5.89823 ( 531) SS BOND : bond 0.00436 ( 6) SS BOND : angle 1.00306 ( 12) covalent geometry : bond 0.00376 ( 6219) covalent geometry : angle 0.62979 ( 8452) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 90 ASP cc_start: 0.6254 (m-30) cc_final: 0.5410 (m-30) REVERT: F 158 ARG cc_start: 0.8370 (mtt-85) cc_final: 0.7841 (tmt170) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 1.5206 time to fit residues: 229.1531 Evaluate side-chains 78 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 3.9990 chunk 57 optimal weight: 0.0870 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.089809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.059456 restraints weight = 16576.784| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 4.03 r_work: 0.2948 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6230 Z= 0.172 Angle : 0.660 8.247 8479 Z= 0.341 Chirality : 0.045 0.186 946 Planarity : 0.005 0.055 1080 Dihedral : 5.822 49.729 934 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.50 % Allowed : 12.28 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.32 (0.30), residues: 747 helix: 0.36 (1.24), residues: 16 sheet: 1.15 (0.32), residues: 280 loop : -1.21 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.004 0.001 HIS B 35 PHE 0.017 0.002 PHE A 118 TYR 0.015 0.001 TYR A 140 ARG 0.006 0.001 ARG D 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00375 ( 5) link_NAG-ASN : angle 2.01132 ( 15) hydrogen bonds : bond 0.03875 ( 195) hydrogen bonds : angle 4.99169 ( 531) SS BOND : bond 0.00396 ( 6) SS BOND : angle 1.19223 ( 12) covalent geometry : bond 0.00414 ( 6219) covalent geometry : angle 0.65442 ( 8452) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1 GLN cc_start: 0.8419 (pt0) cc_final: 0.7878 (pp30) REVERT: D 73 ASP cc_start: 0.8417 (t0) cc_final: 0.8087 (t0) REVERT: A 195 GLU cc_start: 0.8140 (tt0) cc_final: 0.7929 (tm-30) REVERT: B 89 ASP cc_start: 0.8868 (m-30) cc_final: 0.8618 (m-30) REVERT: F 158 ARG cc_start: 0.8812 (mtt-85) cc_final: 0.7478 (tmt170) REVERT: F 169 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8414 (tp30) REVERT: F 298 GLU cc_start: 0.8163 (tp30) cc_final: 0.7949 (tp30) outliers start: 10 outliers final: 5 residues processed: 95 average time/residue: 1.2560 time to fit residues: 124.8913 Evaluate side-chains 80 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain F residue 169 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 1 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.089757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.059437 restraints weight = 16831.631| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 4.09 r_work: 0.2941 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6230 Z= 0.129 Angle : 0.624 8.104 8479 Z= 0.316 Chirality : 0.045 0.182 946 Planarity : 0.005 0.051 1080 Dihedral : 5.157 34.540 934 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.25 % Allowed : 13.47 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.30), residues: 747 helix: 0.96 (1.38), residues: 16 sheet: 1.24 (0.32), residues: 280 loop : -1.08 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.015 0.001 PHE A 118 TYR 0.014 0.001 TYR A 192 ARG 0.006 0.001 ARG D 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 5) link_NAG-ASN : angle 1.87473 ( 15) hydrogen bonds : bond 0.03244 ( 195) hydrogen bonds : angle 4.70986 ( 531) SS BOND : bond 0.00325 ( 6) SS BOND : angle 0.96941 ( 12) covalent geometry : bond 0.00312 ( 6219) covalent geometry : angle 0.61901 ( 8452) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 ASP cc_start: 0.8502 (t0) cc_final: 0.8150 (t0) REVERT: D 90 ASP cc_start: 0.8234 (t70) cc_final: 0.8001 (t70) REVERT: A 108 ARG cc_start: 0.8270 (tmm-80) cc_final: 0.7892 (tpt-90) REVERT: A 147 GLN cc_start: 0.7704 (tp40) cc_final: 0.7425 (tp-100) REVERT: A 195 GLU cc_start: 0.8159 (tt0) cc_final: 0.7913 (tm-30) REVERT: B 89 ASP cc_start: 0.8863 (m-30) cc_final: 0.8491 (m-30) REVERT: F 100 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8372 (mp) REVERT: F 158 ARG cc_start: 0.8794 (mtt-85) cc_final: 0.7465 (tmt170) REVERT: F 169 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8366 (tp30) REVERT: F 298 GLU cc_start: 0.8169 (tp30) cc_final: 0.7922 (tp30) outliers start: 15 outliers final: 7 residues processed: 89 average time/residue: 1.3811 time to fit residues: 128.6553 Evaluate side-chains 83 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 169 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 74 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 52 optimal weight: 0.0010 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN F 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.088982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.059035 restraints weight = 16954.907| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 4.06 r_work: 0.2931 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6230 Z= 0.132 Angle : 0.623 10.252 8479 Z= 0.314 Chirality : 0.044 0.180 946 Planarity : 0.005 0.050 1080 Dihedral : 4.857 33.434 934 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.69 % Allowed : 14.67 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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 (0.31), residues: 747 helix: 0.94 (1.41), residues: 16 sheet: 1.20 (0.32), residues: 282 loop : -0.99 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.018 0.001 PHE B 130 TYR 0.013 0.001 TYR B 94 ARG 0.008 0.001 ARG D 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 5) link_NAG-ASN : angle 1.87066 ( 15) hydrogen bonds : bond 0.03093 ( 195) hydrogen bonds : angle 4.61050 ( 531) SS BOND : bond 0.00313 ( 6) SS BOND : angle 0.97993 ( 12) covalent geometry : bond 0.00324 ( 6219) covalent geometry : angle 0.61767 ( 8452) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 73 ASP cc_start: 0.8567 (t0) cc_final: 0.8052 (t0) REVERT: A 147 GLN cc_start: 0.7728 (tp40) cc_final: 0.7441 (tp-100) REVERT: A 195 GLU cc_start: 0.8192 (tt0) cc_final: 0.7942 (tm-30) REVERT: B 89 ASP cc_start: 0.8912 (m-30) cc_final: 0.8473 (m-30) REVERT: F 100 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8328 (mp) REVERT: F 158 ARG cc_start: 0.8792 (mtt-85) cc_final: 0.7480 (tmt170) REVERT: F 169 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8400 (tp30) REVERT: F 298 GLU cc_start: 0.8138 (tp30) cc_final: 0.7885 (tp30) outliers start: 18 outliers final: 7 residues processed: 86 average time/residue: 1.2654 time to fit residues: 114.2107 Evaluate side-chains 77 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 169 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 32 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 0.0470 chunk 4 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN F 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.089169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.059083 restraints weight = 16835.673| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 4.04 r_work: 0.2937 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6230 Z= 0.129 Angle : 0.614 8.443 8479 Z= 0.312 Chirality : 0.044 0.178 946 Planarity : 0.005 0.049 1080 Dihedral : 4.599 32.011 934 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.10 % Allowed : 15.72 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.31), residues: 747 helix: 0.96 (1.41), residues: 16 sheet: 1.17 (0.31), residues: 284 loop : -0.96 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.012 0.001 PHE B 130 TYR 0.013 0.001 TYR B 94 ARG 0.008 0.001 ARG D 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 5) link_NAG-ASN : angle 1.81553 ( 15) hydrogen bonds : bond 0.02968 ( 195) hydrogen bonds : angle 4.48709 ( 531) SS BOND : bond 0.00323 ( 6) SS BOND : angle 0.98829 ( 12) covalent geometry : bond 0.00317 ( 6219) covalent geometry : angle 0.60916 ( 8452) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: D 73 ASP cc_start: 0.8786 (t0) cc_final: 0.8262 (t0) REVERT: D 76 LYS cc_start: 0.9304 (mtmt) cc_final: 0.8998 (pttp) REVERT: A 105 ASP cc_start: 0.8062 (m-30) cc_final: 0.7822 (p0) REVERT: A 108 ARG cc_start: 0.8192 (tmm-80) cc_final: 0.7785 (tpt-90) REVERT: A 147 GLN cc_start: 0.7715 (tp40) cc_final: 0.7424 (tp-100) REVERT: A 195 GLU cc_start: 0.8221 (tt0) cc_final: 0.7978 (tm-30) REVERT: B 89 ASP cc_start: 0.8947 (m-30) cc_final: 0.8511 (m-30) REVERT: B 125 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8336 (tmmm) REVERT: B 154 ASP cc_start: 0.8460 (m-30) cc_final: 0.7890 (m-30) REVERT: F 24 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8118 (mp) REVERT: F 158 ARG cc_start: 0.8779 (mtt-85) cc_final: 0.7446 (tpt170) REVERT: F 169 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8412 (tp30) REVERT: F 298 GLU cc_start: 0.8035 (tp30) cc_final: 0.7796 (tp30) outliers start: 14 outliers final: 8 residues processed: 86 average time/residue: 1.5031 time to fit residues: 135.1542 Evaluate side-chains 76 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 197 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 9 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN F 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.086884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.056791 restraints weight = 16781.141| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 4.01 r_work: 0.2882 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6230 Z= 0.217 Angle : 0.694 8.968 8479 Z= 0.357 Chirality : 0.046 0.188 946 Planarity : 0.005 0.051 1080 Dihedral : 5.063 35.502 934 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.14 % Allowed : 17.07 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.17 (0.31), residues: 747 helix: 0.96 (1.44), residues: 16 sheet: 1.04 (0.31), residues: 298 loop : -1.05 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.005 0.001 HIS B 35 PHE 0.016 0.002 PHE B 156 TYR 0.016 0.001 TYR B 94 ARG 0.011 0.001 ARG D 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 5) link_NAG-ASN : angle 1.93809 ( 15) hydrogen bonds : bond 0.03771 ( 195) hydrogen bonds : angle 4.87063 ( 531) SS BOND : bond 0.00471 ( 6) SS BOND : angle 1.41483 ( 12) covalent geometry : bond 0.00529 ( 6219) covalent geometry : angle 0.68854 ( 8452) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 ASP cc_start: 0.8766 (t0) cc_final: 0.8107 (t0) REVERT: D 76 LYS cc_start: 0.9293 (mtmt) cc_final: 0.8979 (mtmt) REVERT: A 108 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7696 (tpt-90) REVERT: A 147 GLN cc_start: 0.7830 (tp40) cc_final: 0.7500 (tp-100) REVERT: A 161 GLU cc_start: 0.8981 (pm20) cc_final: 0.8742 (mm-30) REVERT: A 195 GLU cc_start: 0.8391 (tt0) cc_final: 0.8143 (tm-30) REVERT: B 89 ASP cc_start: 0.9048 (m-30) cc_final: 0.8647 (m-30) REVERT: F 24 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8119 (mp) REVERT: F 100 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8583 (OUTLIER) REVERT: F 158 ARG cc_start: 0.8770 (mtt-85) cc_final: 0.7489 (tmt170) REVERT: F 169 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8131 (tm-30) REVERT: F 298 GLU cc_start: 0.8011 (tp30) cc_final: 0.7794 (tp30) outliers start: 21 outliers final: 14 residues processed: 83 average time/residue: 1.3316 time to fit residues: 115.4856 Evaluate side-chains 83 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 GLN Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 169 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 71 optimal weight: 3.9990 chunk 68 optimal weight: 0.0870 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.088419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.058490 restraints weight = 16897.209| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 4.00 r_work: 0.2918 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6230 Z= 0.129 Angle : 0.639 8.636 8479 Z= 0.327 Chirality : 0.044 0.188 946 Planarity : 0.005 0.050 1080 Dihedral : 4.668 32.889 934 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.14 % Allowed : 17.22 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.31), residues: 747 helix: 1.10 (1.45), residues: 16 sheet: 1.07 (0.30), residues: 300 loop : -0.96 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.016 0.001 PHE A 118 TYR 0.013 0.001 TYR B 94 ARG 0.014 0.001 ARG D 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00361 ( 5) link_NAG-ASN : angle 1.60246 ( 15) hydrogen bonds : bond 0.02846 ( 195) hydrogen bonds : angle 4.60665 ( 531) SS BOND : bond 0.00286 ( 6) SS BOND : angle 1.20079 ( 12) covalent geometry : bond 0.00320 ( 6219) covalent geometry : angle 0.63479 ( 8452) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 1.167 Fit side-chains revert: symmetry clash REVERT: D 73 ASP cc_start: 0.8759 (t0) cc_final: 0.8312 (t0) REVERT: A 105 ASP cc_start: 0.8034 (m-30) cc_final: 0.7722 (p0) REVERT: A 108 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7838 (tpt-90) REVERT: A 147 GLN cc_start: 0.7799 (tp40) cc_final: 0.7473 (tp-100) REVERT: A 161 GLU cc_start: 0.9013 (pm20) cc_final: 0.8704 (mm-30) REVERT: A 183 LYS cc_start: 0.5218 (OUTLIER) cc_final: 0.4844 (mmtp) REVERT: A 195 GLU cc_start: 0.8452 (tt0) cc_final: 0.8214 (tm-30) REVERT: B 89 ASP cc_start: 0.9009 (m-30) cc_final: 0.8551 (m-30) REVERT: B 125 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8326 (tmmm) REVERT: B 154 ASP cc_start: 0.8407 (m-30) cc_final: 0.7810 (m-30) REVERT: F 24 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8120 (mp) REVERT: F 158 ARG cc_start: 0.8722 (mtt-85) cc_final: 0.7413 (tpt170) outliers start: 21 outliers final: 12 residues processed: 86 average time/residue: 2.1894 time to fit residues: 197.3592 Evaluate side-chains 82 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 GLN Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain F residue 24 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 26 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 5 optimal weight: 0.0050 chunk 48 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 70 optimal weight: 0.1980 chunk 72 optimal weight: 3.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.088927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.059058 restraints weight = 16736.844| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.99 r_work: 0.2935 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6230 Z= 0.123 Angle : 0.648 10.090 8479 Z= 0.331 Chirality : 0.044 0.180 946 Planarity : 0.005 0.050 1080 Dihedral : 4.508 31.804 934 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.25 % Allowed : 18.71 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.02 (0.31), residues: 747 helix: 1.25 (1.45), residues: 16 sheet: 1.16 (0.31), residues: 298 loop : -0.97 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.020 0.001 PHE A 118 TYR 0.013 0.001 TYR B 94 ARG 0.012 0.001 ARG D 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 5) link_NAG-ASN : angle 1.59687 ( 15) hydrogen bonds : bond 0.02759 ( 195) hydrogen bonds : angle 4.53553 ( 531) SS BOND : bond 0.00274 ( 6) SS BOND : angle 1.13003 ( 12) covalent geometry : bond 0.00304 ( 6219) covalent geometry : angle 0.64369 ( 8452) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: D 73 ASP cc_start: 0.8745 (t0) cc_final: 0.8274 (t0) REVERT: D 112 GLN cc_start: 0.8275 (mp10) cc_final: 0.8041 (pm20) REVERT: A 105 ASP cc_start: 0.7929 (m-30) cc_final: 0.7718 (p0) REVERT: A 108 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7889 (tpt-90) REVERT: A 147 GLN cc_start: 0.7786 (tp40) cc_final: 0.7463 (tp-100) REVERT: A 161 GLU cc_start: 0.9001 (pm20) cc_final: 0.8641 (mm-30) REVERT: A 195 GLU cc_start: 0.8457 (tt0) cc_final: 0.8217 (tm-30) REVERT: B 89 ASP cc_start: 0.8993 (m-30) cc_final: 0.8546 (m-30) REVERT: B 125 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8328 (tmmm) REVERT: B 154 ASP cc_start: 0.8362 (m-30) cc_final: 0.7748 (m-30) REVERT: F 24 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8112 (mp) REVERT: F 158 ARG cc_start: 0.8711 (mtt-85) cc_final: 0.7402 (tpt170) outliers start: 15 outliers final: 7 residues processed: 81 average time/residue: 1.3591 time to fit residues: 115.5240 Evaluate side-chains 76 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain F residue 24 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.086056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.056112 restraints weight = 17210.652| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 4.02 r_work: 0.2859 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 6230 Z= 0.282 Angle : 0.757 10.838 8479 Z= 0.389 Chirality : 0.047 0.213 946 Planarity : 0.005 0.066 1080 Dihedral : 5.282 36.222 934 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.95 % Allowed : 19.31 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.30), residues: 747 helix: 1.25 (1.47), residues: 16 sheet: 0.70 (0.31), residues: 297 loop : -0.97 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 47 HIS 0.006 0.001 HIS B 35 PHE 0.024 0.002 PHE F 220 TYR 0.030 0.002 TYR A 186 ARG 0.015 0.001 ARG D 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00459 ( 5) link_NAG-ASN : angle 1.86868 ( 15) hydrogen bonds : bond 0.04065 ( 195) hydrogen bonds : angle 4.94867 ( 531) SS BOND : bond 0.00541 ( 6) SS BOND : angle 1.51338 ( 12) covalent geometry : bond 0.00688 ( 6219) covalent geometry : angle 0.75167 ( 8452) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: D 73 ASP cc_start: 0.8821 (t0) cc_final: 0.8390 (t0) REVERT: A 108 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7951 (tpt-90) REVERT: A 147 GLN cc_start: 0.7928 (tp40) cc_final: 0.7715 (tp40) REVERT: A 161 GLU cc_start: 0.9065 (pm20) cc_final: 0.8587 (mm-30) REVERT: A 195 GLU cc_start: 0.8541 (tt0) cc_final: 0.8296 (tm-30) REVERT: B 89 ASP cc_start: 0.9070 (m-30) cc_final: 0.8679 (m-30) REVERT: B 125 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8370 (tmmm) REVERT: B 154 ASP cc_start: 0.8516 (m-30) cc_final: 0.7814 (m-30) REVERT: F 24 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8113 (mp) REVERT: F 158 ARG cc_start: 0.8771 (mtt-85) cc_final: 0.7441 (tpt170) outliers start: 13 outliers final: 9 residues processed: 73 average time/residue: 1.2852 time to fit residues: 98.2842 Evaluate side-chains 73 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 GLN Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain F residue 24 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 28 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 0.0870 chunk 70 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.087379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.057454 restraints weight = 17101.847| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 4.02 r_work: 0.2901 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6230 Z= 0.163 Angle : 0.710 10.142 8479 Z= 0.363 Chirality : 0.046 0.205 946 Planarity : 0.005 0.056 1080 Dihedral : 4.986 34.404 934 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.35 % Allowed : 20.06 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.19 (0.31), residues: 747 helix: 1.04 (1.44), residues: 16 sheet: 0.97 (0.31), residues: 300 loop : -1.04 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.004 0.001 HIS B 35 PHE 0.015 0.001 PHE F 220 TYR 0.014 0.001 TYR B 94 ARG 0.014 0.001 ARG D 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 5) link_NAG-ASN : angle 1.55694 ( 15) hydrogen bonds : bond 0.03248 ( 195) hydrogen bonds : angle 4.78219 ( 531) SS BOND : bond 0.00388 ( 6) SS BOND : angle 0.99404 ( 12) covalent geometry : bond 0.00406 ( 6219) covalent geometry : angle 0.70733 ( 8452) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: D 73 ASP cc_start: 0.8861 (t0) cc_final: 0.8453 (t0) REVERT: D 112 GLN cc_start: 0.8381 (mp10) cc_final: 0.8120 (pm20) REVERT: A 105 ASP cc_start: 0.7959 (m-30) cc_final: 0.7721 (p0) REVERT: A 108 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7836 (tpt-90) REVERT: A 147 GLN cc_start: 0.7816 (tp40) cc_final: 0.7481 (tp-100) REVERT: A 161 GLU cc_start: 0.9072 (pm20) cc_final: 0.8583 (mm-30) REVERT: A 195 GLU cc_start: 0.8567 (tt0) cc_final: 0.8318 (tm-30) REVERT: A 211 ARG cc_start: 0.9089 (ptm-80) cc_final: 0.8836 (mtp-110) REVERT: B 89 ASP cc_start: 0.9037 (m-30) cc_final: 0.8611 (m-30) REVERT: B 125 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8362 (tmmm) REVERT: B 154 ASP cc_start: 0.8445 (m-30) cc_final: 0.7724 (m-30) REVERT: F 158 ARG cc_start: 0.8749 (mtt-85) cc_final: 0.7460 (tmt170) outliers start: 9 outliers final: 7 residues processed: 73 average time/residue: 1.4219 time to fit residues: 108.4864 Evaluate side-chains 74 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 GLN Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 179 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 74 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 34 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 14 optimal weight: 0.0570 chunk 10 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 55 optimal weight: 0.0040 chunk 54 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.4710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.088949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.059450 restraints weight = 17136.534| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.97 r_work: 0.2936 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6230 Z= 0.122 Angle : 0.677 10.457 8479 Z= 0.343 Chirality : 0.044 0.178 946 Planarity : 0.005 0.057 1080 Dihedral : 4.475 31.136 934 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.65 % Allowed : 19.91 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.31), residues: 747 helix: 0.93 (1.38), residues: 16 sheet: 1.10 (0.31), residues: 298 loop : -0.97 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.009 0.001 PHE F 220 TYR 0.031 0.001 TYR A 186 ARG 0.013 0.001 ARG D 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 5) link_NAG-ASN : angle 1.40717 ( 15) hydrogen bonds : bond 0.02679 ( 195) hydrogen bonds : angle 4.46389 ( 531) SS BOND : bond 0.00276 ( 6) SS BOND : angle 0.84507 ( 12) covalent geometry : bond 0.00307 ( 6219) covalent geometry : angle 0.67451 ( 8452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5996.97 seconds wall clock time: 106 minutes 12.89 seconds (6372.89 seconds total)