Starting phenix.real_space_refine on Wed Feb 14 14:18:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eay_27990/02_2024/8eay_27990.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eay_27990/02_2024/8eay_27990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eay_27990/02_2024/8eay_27990.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eay_27990/02_2024/8eay_27990.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eay_27990/02_2024/8eay_27990.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eay_27990/02_2024/8eay_27990.pdb" } resolution = 3.33 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= -0.001 sd= 0.101 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: 5 Type Number sf(0) Gaussians S 33 5.16 5 C 2979 2.51 5 N 814 2.21 5 O 935 1.98 5 H 4718 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9479 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 6062 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 1 Chain: "H" Number of atoms: 1859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1859 Classifications: {'peptide': 121} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "L" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1558 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Time building chain proxies: 5.10, per 1000 atoms: 0.54 Number of scatterers: 9479 At special positions: 0 Unit cell: (74.37, 85.47, 134.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 O 935 8.00 N 814 7.00 C 2979 6.00 H 4718 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 407 " distance=2.13 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.12 Conformation dependent library (CDL) restraints added in 1.1 seconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1150 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 12 sheets defined 18.1% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 67 through 89 removed outlier: 3.590A pdb=" N ASP A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 130 removed outlier: 3.790A pdb=" N VAL A 118 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 141 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 188 through 196 removed outlier: 4.338A pdb=" N SER A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 237 through 247 removed outlier: 3.865A pdb=" N ILE A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 254 Processing helix chain 'A' and resid 346 through 351 removed outlier: 4.058A pdb=" N GLU A 349 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN A 351 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.774A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 24 removed outlier: 4.353A pdb=" N GLY A 34 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N CYS A 283 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TRP A 309 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 320 " --> pdb=" O TRP A 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 149 removed outlier: 3.523A pdb=" N ALA A 147 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 159 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU A 39 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE A 275 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TRP A 43 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU A 273 " --> pdb=" O TRP A 43 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR A 45 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 271 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL A 47 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR A 269 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR A 49 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL A 267 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N SER A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL A 262 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE A 268 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 149 removed outlier: 3.523A pdb=" N ALA A 147 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 159 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS A 332 " --> pdb=" O ARG A 329 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 327 " --> pdb=" O PHE A 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 374 removed outlier: 3.645A pdb=" N VAL A 382 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 408 " --> pdb=" O VAL A 382 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 399 through 402 removed outlier: 3.595A pdb=" N ILE A 400 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE A 392 " --> pdb=" O ILE A 400 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.747A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.589A pdb=" N ILE H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 9 through 12 removed outlier: 7.166A pdb=" N VAL L 11 " --> pdb=" O THR L 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AB2, first strand: chain 'L' and resid 35 through 37 removed outlier: 6.907A pdb=" N TRP L 35 " --> pdb=" O ILE L 47 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE L 47 " --> pdb=" O TRP L 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 89 through 90 removed outlier: 3.892A pdb=" N VAL L 96 " --> pdb=" O ALA L 90 " (cutoff:3.500A) 150 hydrogen bonds defined for protein. 390 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: 3.27 Time building geometry restraints manager: 7.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4715 1.04 - 1.24: 565 1.24 - 1.43: 1481 1.43 - 1.63: 2752 1.63 - 1.83: 46 Bond restraints: 9559 Sorted by residual: bond pdb=" C PRO H 100C" pdb=" O PRO H 100C" ideal model delta sigma weight residual 1.235 1.062 0.173 1.30e-02 5.92e+03 1.77e+02 bond pdb=" C SER A 27 " pdb=" N CYS A 28 " ideal model delta sigma weight residual 1.332 1.509 -0.177 1.40e-02 5.10e+03 1.59e+02 bond pdb=" C CYS A 28 " pdb=" N SER A 29 " ideal model delta sigma weight residual 1.331 1.468 -0.137 1.41e-02 5.03e+03 9.48e+01 bond pdb=" C GLY A 406 " pdb=" N CYS A 407 " ideal model delta sigma weight residual 1.331 1.449 -0.118 1.37e-02 5.33e+03 7.45e+01 bond pdb=" N PRO H 100C" pdb=" CA PRO H 100C" ideal model delta sigma weight residual 1.469 1.370 0.099 1.28e-02 6.10e+03 5.97e+01 ... (remaining 9554 not shown) Histogram of bond angle deviations from ideal: 65.87 - 80.51: 2 80.51 - 95.15: 1 95.15 - 109.79: 8530 109.79 - 124.43: 8458 124.43 - 139.07: 264 Bond angle restraints: 17255 Sorted by residual: angle pdb=" C PRO H 9 " pdb=" CA PRO H 9 " pdb=" HA PRO H 9 " ideal model delta sigma weight residual 109.00 65.87 43.13 3.00e+00 1.11e-01 2.07e+02 angle pdb=" N PRO H 9 " pdb=" CA PRO H 9 " pdb=" C PRO H 9 " ideal model delta sigma weight residual 112.47 139.07 -26.60 2.06e+00 2.36e-01 1.67e+02 angle pdb=" C MET L 46 " pdb=" N ILE L 47 " pdb=" CA ILE L 47 " ideal model delta sigma weight residual 123.16 136.84 -13.68 1.06e+00 8.90e-01 1.66e+02 angle pdb=" CA SER H 100 " pdb=" C SER H 100 " pdb=" N GLY H 100A" ideal model delta sigma weight residual 115.51 127.24 -11.73 1.08e+00 8.57e-01 1.18e+02 angle pdb=" N GLY H 10 " pdb=" CA GLY H 10 " pdb=" HA2 GLY H 10 " ideal model delta sigma weight residual 110.00 78.56 31.44 3.00e+00 1.11e-01 1.10e+02 ... (remaining 17250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4075 17.88 - 35.77: 299 35.77 - 53.65: 116 53.65 - 71.54: 34 71.54 - 89.42: 11 Dihedral angle restraints: 4535 sinusoidal: 2498 harmonic: 2037 Sorted by residual: dihedral pdb=" N PRO H 9 " pdb=" C PRO H 9 " pdb=" CA PRO H 9 " pdb=" CB PRO H 9 " ideal model delta harmonic sigma weight residual 115.10 157.65 -42.55 0 2.50e+00 1.60e-01 2.90e+02 dihedral pdb=" C PRO H 9 " pdb=" N PRO H 9 " pdb=" CA PRO H 9 " pdb=" CB PRO H 9 " ideal model delta harmonic sigma weight residual -120.70 -159.13 38.43 0 2.50e+00 1.60e-01 2.36e+02 dihedral pdb=" CB CYS A 113 " pdb=" SG CYS A 113 " pdb=" SG CYS A 339 " pdb=" CB CYS A 339 " ideal model delta sinusoidal sigma weight residual 93.00 11.25 81.75 1 1.00e+01 1.00e-02 8.22e+01 ... (remaining 4532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.388: 758 0.388 - 0.777: 0 0.777 - 1.165: 0 1.165 - 1.553: 0 1.553 - 1.942: 1 Chirality restraints: 759 Sorted by residual: chirality pdb=" CA PRO H 9 " pdb=" N PRO H 9 " pdb=" C PRO H 9 " pdb=" CB PRO H 9 " both_signs ideal model delta sigma weight residual False 2.72 0.78 1.94 2.00e-01 2.50e+01 9.43e+01 chirality pdb=" CA MET H 100B" pdb=" N MET H 100B" pdb=" C MET H 100B" pdb=" CB MET H 100B" both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA GLN L 50 " pdb=" N GLN L 50 " pdb=" C GLN L 50 " pdb=" CB GLN L 50 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 756 not shown) Planarity restraints: 1439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN L 38 " -0.008 2.00e-02 2.50e+03 4.30e-01 2.77e+03 pdb=" CD GLN L 38 " -0.001 2.00e-02 2.50e+03 pdb=" OE1 GLN L 38 " 0.008 2.00e-02 2.50e+03 pdb=" NE2 GLN L 38 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN L 38 " -0.744 2.00e-02 2.50e+03 pdb="HE22 GLN L 38 " 0.745 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 382 " 0.032 2.00e-02 2.50e+03 5.87e-02 3.44e+01 pdb=" N ALA A 383 " -0.101 2.00e-02 2.50e+03 pdb=" CA ALA A 383 " 0.026 2.00e-02 2.50e+03 pdb=" H ALA A 383 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL L 45 " -0.028 2.00e-02 2.50e+03 5.31e-02 2.82e+01 pdb=" C VAL L 45 " 0.092 2.00e-02 2.50e+03 pdb=" O VAL L 45 " -0.033 2.00e-02 2.50e+03 pdb=" N MET L 46 " -0.031 2.00e-02 2.50e+03 ... (remaining 1436 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 219 2.06 - 2.69: 14539 2.69 - 3.33: 25347 3.33 - 3.96: 33012 3.96 - 4.60: 50197 Nonbonded interactions: 123314 Sorted by model distance: nonbonded pdb=" HH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 1.420 1.850 nonbonded pdb=" HB3 CYS A 113 " pdb=" HB2 CYS A 339 " model vdw 1.454 2.440 nonbonded pdb=" O TYR A 263 " pdb=" HG SER A 266 " model vdw 1.522 1.850 nonbonded pdb="HE22 GLN A 88 " pdb=" O ALA A 211 " model vdw 1.551 1.850 nonbonded pdb=" OE1 GLN L 37 " pdb=" HZ2 LYS L 39 " model vdw 1.560 1.850 ... (remaining 123309 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.150 Extract box with map and model: 4.050 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 33.140 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 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 : 0.008 0.177 4841 Z= 0.533 Angle : 1.137 26.597 6566 Z= 0.693 Chirality : 0.089 1.942 759 Planarity : 0.008 0.111 841 Dihedral : 14.180 76.735 1766 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.55 % Favored : 90.13 % Rotamer: Outliers : 0.76 % Allowed : 2.08 % Favored : 97.16 % Cbeta Deviations : 0.70 % 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: -2.33 (0.34), residues: 618 helix: -1.12 (0.52), residues: 101 sheet: -0.77 (0.42), residues: 172 loop : -2.15 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 309 HIS 0.001 0.000 HIS A 332 PHE 0.007 0.001 PHE A 334 TYR 0.017 0.002 TYR L 2 ARG 0.004 0.000 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 77 average time/residue: 0.3589 time to fit residues: 35.6799 Evaluate side-chains 50 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4841 Z= 0.212 Angle : 0.629 9.598 6566 Z= 0.335 Chirality : 0.045 0.142 759 Planarity : 0.005 0.048 841 Dihedral : 5.031 24.416 676 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.52 % Favored : 89.32 % Rotamer: Outliers : 1.89 % Allowed : 6.99 % Favored : 91.12 % 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: -2.13 (0.34), residues: 618 helix: -0.27 (0.54), residues: 107 sheet: -0.68 (0.42), residues: 164 loop : -2.24 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP H 34 HIS 0.001 0.001 HIS A 368 PHE 0.009 0.001 PHE L 97 TYR 0.021 0.002 TYR H 50 ARG 0.003 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 62 average time/residue: 0.3516 time to fit residues: 28.3231 Evaluate side-chains 57 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain L residue 1 SER Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 15 optimal weight: 3.9990 chunk 55 optimal weight: 0.2980 chunk 59 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4841 Z= 0.185 Angle : 0.575 8.820 6566 Z= 0.305 Chirality : 0.044 0.144 759 Planarity : 0.004 0.046 841 Dihedral : 4.799 21.631 676 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.90 % Favored : 90.94 % Rotamer: Outliers : 1.32 % Allowed : 10.21 % Favored : 88.47 % 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: -2.06 (0.34), residues: 618 helix: 0.27 (0.56), residues: 105 sheet: -0.90 (0.40), residues: 180 loop : -2.25 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 309 HIS 0.001 0.000 HIS A 368 PHE 0.007 0.001 PHE L 97 TYR 0.015 0.001 TYR H 50 ARG 0.002 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 THR cc_start: 0.6366 (p) cc_final: 0.6134 (p) outliers start: 7 outliers final: 7 residues processed: 58 average time/residue: 0.3682 time to fit residues: 27.6887 Evaluate side-chains 56 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 1 SER Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 0.0470 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 49 optimal weight: 0.8980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4841 Z= 0.170 Angle : 0.549 8.655 6566 Z= 0.291 Chirality : 0.043 0.139 759 Planarity : 0.004 0.044 841 Dihedral : 4.666 22.531 676 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.19 % Favored : 89.64 % Rotamer: Outliers : 1.70 % Allowed : 11.34 % Favored : 86.96 % 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: -1.98 (0.34), residues: 618 helix: 0.50 (0.57), residues: 105 sheet: -0.94 (0.38), residues: 186 loop : -2.21 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 47 HIS 0.002 0.001 HIS A 368 PHE 0.007 0.001 PHE L 97 TYR 0.015 0.001 TYR H 50 ARG 0.002 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 2 TYR cc_start: 0.6862 (t80) cc_final: 0.5798 (t80) outliers start: 9 outliers final: 9 residues processed: 56 average time/residue: 0.3761 time to fit residues: 27.1246 Evaluate side-chains 58 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 1 SER Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4841 Z= 0.270 Angle : 0.628 8.435 6566 Z= 0.335 Chirality : 0.045 0.143 759 Planarity : 0.005 0.048 841 Dihedral : 5.020 22.820 676 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.14 % Favored : 87.70 % Rotamer: Outliers : 2.27 % Allowed : 13.42 % Favored : 84.31 % 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: -2.15 (0.34), residues: 618 helix: 0.51 (0.56), residues: 105 sheet: -1.07 (0.38), residues: 185 loop : -2.37 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP H 103 HIS 0.001 0.000 HIS A 332 PHE 0.010 0.002 PHE H 51 TYR 0.022 0.002 TYR H 33 ARG 0.005 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LYS cc_start: 0.8153 (tmmt) cc_final: 0.7947 (pttp) outliers start: 12 outliers final: 11 residues processed: 61 average time/residue: 0.3909 time to fit residues: 30.9831 Evaluate side-chains 62 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 1 SER Chi-restraints excluded: chain L residue 50 GLN Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 59 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4841 Z= 0.205 Angle : 0.561 7.648 6566 Z= 0.299 Chirality : 0.044 0.145 759 Planarity : 0.004 0.046 841 Dihedral : 4.924 22.914 676 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.36 % Favored : 89.48 % Rotamer: Outliers : 1.89 % Allowed : 14.56 % Favored : 83.55 % 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: -2.09 (0.34), residues: 618 helix: 0.53 (0.56), residues: 105 sheet: -0.86 (0.40), residues: 173 loop : -2.40 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.001 0.000 HIS A 368 PHE 0.007 0.001 PHE L 97 TYR 0.016 0.002 TYR A 359 ARG 0.002 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7748 (tmmt) cc_final: 0.7456 (ttmm) REVERT: L 2 TYR cc_start: 0.6877 (t80) cc_final: 0.5661 (t80) outliers start: 10 outliers final: 9 residues processed: 63 average time/residue: 0.3807 time to fit residues: 30.6382 Evaluate side-chains 62 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 1 SER Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 0.0770 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4841 Z= 0.201 Angle : 0.569 6.790 6566 Z= 0.303 Chirality : 0.044 0.144 759 Planarity : 0.004 0.045 841 Dihedral : 4.850 21.227 676 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.33 % Favored : 88.51 % Rotamer: Outliers : 2.27 % Allowed : 14.56 % Favored : 83.18 % 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: -2.14 (0.34), residues: 618 helix: 0.55 (0.56), residues: 105 sheet: -1.04 (0.39), residues: 180 loop : -2.37 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.000 0.000 HIS A 368 PHE 0.006 0.001 PHE L 97 TYR 0.016 0.002 TYR H 50 ARG 0.002 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7748 (tmmt) cc_final: 0.7460 (ttmm) REVERT: L 2 TYR cc_start: 0.6728 (t80) cc_final: 0.6196 (t80) outliers start: 12 outliers final: 12 residues processed: 63 average time/residue: 0.3823 time to fit residues: 30.5874 Evaluate side-chains 67 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain L residue 1 SER Chi-restraints excluded: chain L residue 50 GLN Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 7.9990 chunk 37 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 54 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4841 Z= 0.196 Angle : 0.556 6.448 6566 Z= 0.296 Chirality : 0.044 0.146 759 Planarity : 0.004 0.045 841 Dihedral : 4.851 22.256 676 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.68 % Favored : 89.16 % Rotamer: Outliers : 2.46 % Allowed : 15.12 % Favored : 82.42 % 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: -2.11 (0.34), residues: 618 helix: 0.55 (0.56), residues: 105 sheet: -1.01 (0.39), residues: 180 loop : -2.36 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.001 0.000 HIS A 368 PHE 0.006 0.001 PHE L 97 TYR 0.016 0.002 TYR H 50 ARG 0.002 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7775 (tmmt) cc_final: 0.7532 (ttmm) REVERT: A 142 LYS cc_start: 0.8119 (tmmt) cc_final: 0.7822 (pttp) REVERT: L 2 TYR cc_start: 0.6732 (t80) cc_final: 0.6216 (t80) outliers start: 13 outliers final: 13 residues processed: 62 average time/residue: 0.3944 time to fit residues: 31.0339 Evaluate side-chains 63 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 50 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 1 SER Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 50 GLN Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 51 optimal weight: 0.3980 chunk 54 optimal weight: 0.0980 chunk 35 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4841 Z= 0.160 Angle : 0.533 5.813 6566 Z= 0.283 Chirality : 0.043 0.144 759 Planarity : 0.004 0.044 841 Dihedral : 4.706 20.753 676 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.55 % Favored : 90.29 % Rotamer: Outliers : 2.08 % Allowed : 15.88 % Favored : 82.04 % 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: -2.04 (0.34), residues: 618 helix: 0.58 (0.56), residues: 105 sheet: -0.97 (0.39), residues: 181 loop : -2.29 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 309 HIS 0.000 0.000 HIS A 332 PHE 0.006 0.001 PHE L 97 TYR 0.024 0.001 TYR A 359 ARG 0.001 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7783 (tmmt) cc_final: 0.7551 (ttmm) REVERT: H 1 GLN cc_start: 0.6713 (mm110) cc_final: 0.6427 (tm-30) REVERT: L 2 TYR cc_start: 0.6678 (t80) cc_final: 0.6203 (t80) outliers start: 11 outliers final: 11 residues processed: 63 average time/residue: 0.3940 time to fit residues: 31.5589 Evaluate side-chains 65 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 1 SER Chi-restraints excluded: chain L residue 50 GLN Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 0.0670 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 0.0970 chunk 14 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4841 Z= 0.204 Angle : 0.559 5.765 6566 Z= 0.297 Chirality : 0.044 0.145 759 Planarity : 0.004 0.045 841 Dihedral : 4.798 22.275 676 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.65 % Favored : 88.19 % Rotamer: Outliers : 2.65 % Allowed : 15.31 % Favored : 82.04 % 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: -2.09 (0.34), residues: 618 helix: 0.57 (0.56), residues: 105 sheet: -1.05 (0.39), residues: 180 loop : -2.31 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.000 0.000 HIS A 332 PHE 0.006 0.001 PHE L 97 TYR 0.018 0.002 TYR A 359 ARG 0.002 0.000 ARG H 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 THR cc_start: 0.6215 (OUTLIER) cc_final: 0.5831 (m) REVERT: A 68 LYS cc_start: 0.7797 (tmmt) cc_final: 0.7567 (ttmm) REVERT: L 2 TYR cc_start: 0.6783 (t80) cc_final: 0.6204 (t80) REVERT: L 50 GLN cc_start: 0.6619 (OUTLIER) cc_final: 0.5579 (mp10) outliers start: 14 outliers final: 12 residues processed: 62 average time/residue: 0.3914 time to fit residues: 30.8576 Evaluate side-chains 67 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain L residue 1 SER Chi-restraints excluded: chain L residue 50 GLN Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4735 r_free = 0.4735 target = 0.225564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.182899 restraints weight = 16424.941| |-----------------------------------------------------------------------------| r_work (start): 0.4320 rms_B_bonded: 2.46 r_work: 0.4104 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3965 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4841 Z= 0.216 Angle : 0.577 6.338 6566 Z= 0.306 Chirality : 0.044 0.147 759 Planarity : 0.005 0.045 841 Dihedral : 4.863 22.729 676 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.68 % Favored : 89.16 % Rotamer: Outliers : 2.84 % Allowed : 15.69 % Favored : 81.47 % 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: -2.11 (0.34), residues: 618 helix: 0.43 (0.56), residues: 107 sheet: -1.06 (0.38), residues: 186 loop : -2.30 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.000 0.000 HIS A 368 PHE 0.007 0.001 PHE L 97 TYR 0.019 0.002 TYR A 359 ARG 0.002 0.000 ARG H 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3011.99 seconds wall clock time: 53 minutes 46.36 seconds (3226.36 seconds total)