Starting phenix.real_space_refine on Tue Feb 13 07:42:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrp_33416/02_2024/7xrp_33416.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrp_33416/02_2024/7xrp_33416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrp_33416/02_2024/7xrp_33416.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrp_33416/02_2024/7xrp_33416.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrp_33416/02_2024/7xrp_33416.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrp_33416/02_2024/7xrp_33416.pdb" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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 14 5.16 5 C 2655 2.51 5 N 674 2.21 5 O 786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 44": "OE1" <-> "OE2" Residue "F ARG 346": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F ARG 403": "NH1" <-> "NH2" Residue "F ARG 466": "NH1" <-> "NH2" Residue "F GLU 516": "OE1" <-> "OE2" 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: 4129 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1684 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain breaks: 5 Chain: "B" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 935 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "F" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1454 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 9, 'TRANS': 172} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.86, per 1000 atoms: 0.69 Number of scatterers: 4129 At special positions: 0 Unit cell: (73.91, 77.8, 113.588, 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 14 16.00 O 786 8.00 N 674 7.00 C 2655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 165 " " NAG A 402 " - " ASN A 282 " " NAG A 403 " - " ASN A 122 " " NAG F 601 " - " ASN F 343 " Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 780.2 milliseconds 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 952 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 9 sheets defined 5.4% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'B' and resid 62 through 65 removed outlier: 3.510A pdb=" N LYS B 65 " --> pdb=" O ASP B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'F' and resid 338 through 343 removed outlier: 3.959A pdb=" N PHE F 342 " --> pdb=" O PHE F 338 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN F 343 " --> pdb=" O GLY F 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 338 through 343' Processing helix chain 'F' and resid 403 through 410 removed outlier: 3.708A pdb=" N GLU F 406 " --> pdb=" O ARG F 403 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 506 removed outlier: 3.761A pdb=" N GLN F 506 " --> pdb=" O VAL F 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.590A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.713A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.778A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.562A pdb=" N VAL B 79 " --> pdb=" O CYS B 22 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR B 69 " --> pdb=" O GLN B 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.601A pdb=" N THR B 122 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 12 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER B 124 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 121 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 92 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN B 39 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 35 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU B 99 " --> pdb=" O PHE B 33 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N PHE B 33 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.601A pdb=" N THR B 122 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 12 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER B 124 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 121 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 92 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 49 through 50 Processing sheet with id=AA8, first strand: chain 'F' and resid 354 through 357 removed outlier: 5.047A pdb=" N ASN F 394 " --> pdb=" O GLU F 516 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLU F 516 " --> pdb=" O ASN F 394 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU F 513 " --> pdb=" O CYS F 432 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL F 433 " --> pdb=" O LYS F 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 452 through 454 95 hydrogen bonds defined for protein. 219 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: 1.40 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 666 1.30 - 1.44: 1271 1.44 - 1.57: 2278 1.57 - 1.70: 1 1.70 - 1.83: 15 Bond restraints: 4231 Sorted by residual: bond pdb=" CA ALA F 352 " pdb=" C ALA F 352 " ideal model delta sigma weight residual 1.528 1.442 0.086 1.04e-02 9.25e+03 6.82e+01 bond pdb=" CA SER F 349 " pdb=" C SER F 349 " ideal model delta sigma weight residual 1.526 1.425 0.100 1.36e-02 5.41e+03 5.46e+01 bond pdb=" CA ARG F 346 " pdb=" C ARG F 346 " ideal model delta sigma weight residual 1.522 1.446 0.076 1.23e-02 6.61e+03 3.81e+01 bond pdb=" CA PHE F 347 " pdb=" C PHE F 347 " ideal model delta sigma weight residual 1.522 1.449 0.074 1.23e-02 6.61e+03 3.58e+01 bond pdb=" CA ALA F 348 " pdb=" C ALA F 348 " ideal model delta sigma weight residual 1.528 1.456 0.072 1.38e-02 5.25e+03 2.71e+01 ... (remaining 4226 not shown) Histogram of bond angle deviations from ideal: 84.30 - 94.24: 1 94.24 - 104.18: 56 104.18 - 114.13: 2333 114.13 - 124.07: 3257 124.07 - 134.02: 101 Bond angle restraints: 5748 Sorted by residual: angle pdb=" N ARG A 214 " pdb=" CA ARG A 214 " pdb=" C ARG A 214 " ideal model delta sigma weight residual 109.76 84.30 25.46 1.59e+00 3.96e-01 2.56e+02 angle pdb=" N VAL F 350 " pdb=" CA VAL F 350 " pdb=" C VAL F 350 " ideal model delta sigma weight residual 110.62 118.46 -7.84 1.02e+00 9.61e-01 5.90e+01 angle pdb=" N ASN A 122 " pdb=" CA ASN A 122 " pdb=" C ASN A 122 " ideal model delta sigma weight residual 111.28 118.92 -7.64 1.09e+00 8.42e-01 4.91e+01 angle pdb=" N TYR F 473 " pdb=" CA TYR F 473 " pdb=" C TYR F 473 " ideal model delta sigma weight residual 113.38 121.61 -8.23 1.23e+00 6.61e-01 4.47e+01 angle pdb=" N VAL A 130 " pdb=" CA VAL A 130 " pdb=" C VAL A 130 " ideal model delta sigma weight residual 113.10 107.19 5.91 9.70e-01 1.06e+00 3.72e+01 ... (remaining 5743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 2217 17.34 - 34.67: 241 34.67 - 52.01: 47 52.01 - 69.35: 5 69.35 - 86.68: 4 Dihedral angle restraints: 2514 sinusoidal: 1022 harmonic: 1492 Sorted by residual: dihedral pdb=" CA CYS F 336 " pdb=" C CYS F 336 " pdb=" N PRO F 337 " pdb=" CA PRO F 337 " ideal model delta harmonic sigma weight residual -180.00 -148.94 -31.06 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CA ASN F 360 " pdb=" C ASN F 360 " pdb=" N CYS F 361 " pdb=" CA CYS F 361 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA PHE F 490 " pdb=" C PHE F 490 " pdb=" N PRO F 491 " pdb=" CA PRO F 491 " ideal model delta harmonic sigma weight residual -180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 2511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 546 0.095 - 0.190: 71 0.190 - 0.284: 14 0.284 - 0.379: 4 0.379 - 0.474: 4 Chirality restraints: 639 Sorted by residual: chirality pdb=" CA PRO A 217 " pdb=" N PRO A 217 " pdb=" C PRO A 217 " pdb=" CB PRO A 217 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.47 2.00e-01 2.50e+01 5.61e+00 chirality pdb=" CA PHE F 429 " pdb=" N PHE F 429 " pdb=" C PHE F 429 " pdb=" CB PHE F 429 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" CA VAL F 350 " pdb=" N VAL F 350 " pdb=" C VAL F 350 " pdb=" CB VAL F 350 " both_signs ideal model delta sigma weight residual False 2.44 2.03 0.42 2.00e-01 2.50e+01 4.32e+00 ... (remaining 636 not shown) Planarity restraints: 739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 403 " -0.344 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG A 403 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG A 403 " -0.135 2.00e-02 2.50e+03 pdb=" N2 NAG A 403 " 0.529 2.00e-02 2.50e+03 pdb=" O7 NAG A 403 " -0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 401 " -0.316 2.00e-02 2.50e+03 2.74e-01 9.36e+02 pdb=" C7 NAG A 401 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG A 401 " -0.148 2.00e-02 2.50e+03 pdb=" N2 NAG A 401 " 0.488 2.00e-02 2.50e+03 pdb=" O7 NAG A 401 " -0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 601 " -0.276 2.00e-02 2.50e+03 2.30e-01 6.61e+02 pdb=" C7 NAG F 601 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG F 601 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG F 601 " 0.385 2.00e-02 2.50e+03 pdb=" O7 NAG F 601 " 0.000 2.00e-02 2.50e+03 ... (remaining 736 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1059 2.79 - 3.32: 3382 3.32 - 3.84: 6407 3.84 - 4.37: 6913 4.37 - 4.90: 12570 Nonbonded interactions: 30331 Sorted by model distance: nonbonded pdb=" O THR A 51 " pdb=" OG1 THR A 274 " model vdw 2.261 2.440 nonbonded pdb=" N ARG A 214 " pdb=" O ARG A 214 " model vdw 2.271 2.496 nonbonded pdb=" O ASP A 290 " pdb=" OG SER A 297 " model vdw 2.277 2.440 nonbonded pdb=" OG SER F 383 " pdb=" O THR F 385 " model vdw 2.284 2.440 nonbonded pdb=" O SER B 103 " pdb=" OG SER B 103 " model vdw 2.286 2.440 ... (remaining 30326 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 group one per residue 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: 6.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 26.930 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.650 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 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 0.100 4231 Z= 0.501 Angle : 1.139 25.464 5748 Z= 0.701 Chirality : 0.079 0.474 639 Planarity : 0.019 0.297 735 Dihedral : 14.361 86.684 1547 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.45 % Allowed : 12.87 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: -4.63 (0.29), residues: 499 helix: -5.03 (0.29), residues: 24 sheet: -3.31 (0.33), residues: 154 loop : -2.90 (0.28), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP F 436 HIS 0.004 0.001 HIS B 30 PHE 0.036 0.002 PHE F 400 TYR 0.020 0.002 TYR F 351 ARG 0.002 0.001 ARG F 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7900 (mttm) cc_final: 0.7665 (tmtt) REVERT: B 39 GLN cc_start: 0.6561 (tt0) cc_final: 0.6258 (pp30) REVERT: B 115 TRP cc_start: 0.7598 (m100) cc_final: 0.7101 (m100) REVERT: F 355 ARG cc_start: 0.8556 (ttt90) cc_final: 0.8178 (ttm-80) REVERT: F 449 TYR cc_start: 0.8004 (m-80) cc_final: 0.7562 (m-80) REVERT: F 456 PHE cc_start: 0.8398 (m-80) cc_final: 0.8031 (m-80) REVERT: F 498 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7866 (mm-40) outliers start: 2 outliers final: 0 residues processed: 129 average time/residue: 0.2499 time to fit residues: 37.3313 Evaluate side-chains 90 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN B 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4231 Z= 0.294 Angle : 0.705 7.551 5748 Z= 0.368 Chirality : 0.046 0.158 639 Planarity : 0.005 0.038 735 Dihedral : 6.905 59.830 646 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 4.29 % Allowed : 21.44 % Favored : 74.27 % 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: -4.12 (0.33), residues: 499 helix: -4.66 (0.36), residues: 30 sheet: -2.77 (0.34), residues: 181 loop : -2.50 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 436 HIS 0.005 0.001 HIS B 30 PHE 0.022 0.002 PHE A 168 TYR 0.015 0.002 TYR B 80 ARG 0.009 0.001 ARG F 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 0.441 Fit side-chains REVERT: A 227 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8516 (m) REVERT: A 275 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7687 (m-10) REVERT: B 19 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6316 (mtt180) REVERT: B 20 LEU cc_start: 0.8762 (mm) cc_final: 0.8433 (mm) REVERT: B 39 GLN cc_start: 0.6604 (tt0) cc_final: 0.5436 (pp30) REVERT: B 46 GLU cc_start: 0.7154 (tp30) cc_final: 0.6938 (tp30) REVERT: B 115 TRP cc_start: 0.7628 (m100) cc_final: 0.7387 (m100) REVERT: F 355 ARG cc_start: 0.8323 (ttt90) cc_final: 0.7940 (ttm-80) REVERT: F 417 LYS cc_start: 0.8114 (ttmt) cc_final: 0.7912 (ttpp) REVERT: F 423 TYR cc_start: 0.8832 (t80) cc_final: 0.8589 (t80) REVERT: F 444 LYS cc_start: 0.7191 (tptp) cc_final: 0.6896 (tptp) REVERT: F 449 TYR cc_start: 0.7931 (m-80) cc_final: 0.7429 (m-80) REVERT: F 456 PHE cc_start: 0.8504 (m-80) cc_final: 0.8117 (m-80) REVERT: F 465 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8165 (mt-10) REVERT: F 498 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7807 (mm-40) outliers start: 19 outliers final: 9 residues processed: 119 average time/residue: 0.2387 time to fit residues: 32.9977 Evaluate side-chains 100 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 392 PHE Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 465 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN B 30 HIS B 74 ASN B 77 ASN B 113 ASN ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 4231 Z= 0.401 Angle : 0.718 6.248 5748 Z= 0.379 Chirality : 0.047 0.156 639 Planarity : 0.005 0.050 735 Dihedral : 6.782 56.308 646 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 7.00 % Allowed : 23.02 % Favored : 69.98 % 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: -3.92 (0.34), residues: 499 helix: -4.46 (0.44), residues: 30 sheet: -2.70 (0.34), residues: 185 loop : -2.30 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 436 HIS 0.006 0.001 HIS B 30 PHE 0.021 0.002 PHE F 400 TYR 0.023 0.002 TYR A 170 ARG 0.012 0.001 ARG F 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 93 time to evaluate : 0.496 Fit side-chains REVERT: A 170 TYR cc_start: 0.7479 (t80) cc_final: 0.6809 (t80) REVERT: A 214 ARG cc_start: 0.8443 (mtt-85) cc_final: 0.8239 (mtt-85) REVERT: A 275 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7719 (m-10) REVERT: A 296 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8010 (tp) REVERT: B 19 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6266 (mtt180) REVERT: B 20 LEU cc_start: 0.8819 (mm) cc_final: 0.8395 (mm) REVERT: F 340 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8496 (tm-30) REVERT: F 364 ASP cc_start: 0.8187 (p0) cc_final: 0.7770 (p0) REVERT: F 417 LYS cc_start: 0.8056 (ttmt) cc_final: 0.7848 (ttpp) REVERT: F 449 TYR cc_start: 0.7853 (m-80) cc_final: 0.7437 (m-80) REVERT: F 456 PHE cc_start: 0.8600 (m-80) cc_final: 0.8306 (m-80) REVERT: F 498 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7907 (mm-40) outliers start: 31 outliers final: 21 residues processed: 114 average time/residue: 0.2189 time to fit residues: 29.6828 Evaluate side-chains 105 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 81 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 392 PHE Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 487 ASN Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 510 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.0040 chunk 23 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 414 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4231 Z= 0.204 Angle : 0.610 8.178 5748 Z= 0.316 Chirality : 0.044 0.151 639 Planarity : 0.004 0.035 735 Dihedral : 5.681 39.620 646 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 4.74 % Allowed : 27.77 % Favored : 67.49 % 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: -3.70 (0.34), residues: 499 helix: -4.34 (0.46), residues: 30 sheet: -2.56 (0.35), residues: 180 loop : -2.16 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 353 HIS 0.001 0.000 HIS A 49 PHE 0.014 0.001 PHE F 400 TYR 0.017 0.001 TYR A 265 ARG 0.007 0.001 ARG F 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 0.490 Fit side-chains REVERT: A 170 TYR cc_start: 0.7290 (t80) cc_final: 0.7070 (t80) REVERT: A 229 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.7004 (mm) REVERT: A 296 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7974 (tp) REVERT: B 20 LEU cc_start: 0.8817 (mm) cc_final: 0.8460 (mm) REVERT: B 46 GLU cc_start: 0.7107 (tp30) cc_final: 0.6365 (tp30) REVERT: F 417 LYS cc_start: 0.8169 (ttmt) cc_final: 0.7857 (ttpp) REVERT: F 449 TYR cc_start: 0.7829 (m-80) cc_final: 0.7380 (m-80) REVERT: F 498 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7835 (mm-40) outliers start: 21 outliers final: 15 residues processed: 103 average time/residue: 0.2222 time to fit residues: 27.2641 Evaluate side-chains 95 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 408 ARG Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 510 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN B 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4231 Z= 0.324 Angle : 0.658 7.914 5748 Z= 0.339 Chirality : 0.046 0.150 639 Planarity : 0.004 0.030 735 Dihedral : 5.584 25.507 646 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 5.87 % Allowed : 28.67 % Favored : 65.46 % 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: -3.70 (0.35), residues: 499 helix: -4.39 (0.44), residues: 30 sheet: -2.58 (0.35), residues: 179 loop : -2.14 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 353 HIS 0.006 0.001 HIS B 30 PHE 0.019 0.002 PHE F 400 TYR 0.021 0.002 TYR F 369 ARG 0.007 0.001 ARG F 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 79 time to evaluate : 0.491 Fit side-chains REVERT: A 91 TYR cc_start: 0.9086 (t80) cc_final: 0.8810 (t80) REVERT: A 129 LYS cc_start: 0.7561 (ttpt) cc_final: 0.7260 (tttt) REVERT: A 229 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6929 (mm) REVERT: A 296 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8015 (tp) REVERT: B 19 ARG cc_start: 0.6944 (OUTLIER) cc_final: 0.6477 (mtt180) REVERT: B 20 LEU cc_start: 0.8862 (mm) cc_final: 0.8505 (mm) REVERT: F 364 ASP cc_start: 0.8114 (p0) cc_final: 0.7666 (p0) REVERT: F 417 LYS cc_start: 0.8103 (ttmt) cc_final: 0.7805 (ttpp) REVERT: F 498 GLN cc_start: 0.8255 (mm-40) cc_final: 0.7803 (mm-40) outliers start: 26 outliers final: 18 residues processed: 99 average time/residue: 0.2261 time to fit residues: 26.6516 Evaluate side-chains 97 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 76 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 408 ARG Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 46 optimal weight: 0.0670 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4231 Z= 0.206 Angle : 0.593 7.729 5748 Z= 0.306 Chirality : 0.044 0.143 639 Planarity : 0.004 0.028 735 Dihedral : 4.942 22.611 646 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 4.97 % Allowed : 30.93 % Favored : 64.11 % 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: -3.61 (0.35), residues: 499 helix: -4.03 (0.49), residues: 30 sheet: -2.62 (0.34), residues: 185 loop : -2.01 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 436 HIS 0.001 0.000 HIS A 49 PHE 0.016 0.001 PHE F 400 TYR 0.022 0.001 TYR F 369 ARG 0.005 0.001 ARG F 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 0.492 Fit side-chains REVERT: A 129 LYS cc_start: 0.7469 (ttpt) cc_final: 0.7219 (tttt) REVERT: A 229 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6951 (mm) REVERT: A 296 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7923 (tp) REVERT: B 19 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.6710 (mtt180) REVERT: B 20 LEU cc_start: 0.8843 (mm) cc_final: 0.8547 (mm) REVERT: B 46 GLU cc_start: 0.7087 (tp30) cc_final: 0.6329 (tp30) REVERT: F 417 LYS cc_start: 0.8132 (ttmt) cc_final: 0.7851 (ttpp) REVERT: F 449 TYR cc_start: 0.7793 (m-80) cc_final: 0.7429 (m-80) REVERT: F 498 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7856 (mm-40) outliers start: 22 outliers final: 17 residues processed: 96 average time/residue: 0.2187 time to fit residues: 24.9862 Evaluate side-chains 94 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 74 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 392 PHE Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 408 ARG Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN B 30 HIS ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4231 Z= 0.227 Angle : 0.601 7.384 5748 Z= 0.309 Chirality : 0.044 0.146 639 Planarity : 0.004 0.027 735 Dihedral : 4.847 22.325 646 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 5.64 % Allowed : 30.47 % Favored : 63.88 % 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: -3.48 (0.35), residues: 499 helix: -3.95 (0.55), residues: 24 sheet: -2.57 (0.35), residues: 185 loop : -1.95 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 436 HIS 0.006 0.001 HIS B 30 PHE 0.018 0.001 PHE F 400 TYR 0.021 0.001 TYR F 369 ARG 0.005 0.001 ARG F 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 78 time to evaluate : 0.508 Fit side-chains REVERT: A 229 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6941 (mm) REVERT: A 296 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7910 (tp) REVERT: B 19 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6629 (mtt180) REVERT: B 20 LEU cc_start: 0.8861 (mm) cc_final: 0.8560 (mm) REVERT: B 30 HIS cc_start: 0.7922 (OUTLIER) cc_final: 0.7629 (m-70) REVERT: F 417 LYS cc_start: 0.8229 (ttmt) cc_final: 0.7959 (ttpp) REVERT: F 498 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7810 (mm-40) outliers start: 25 outliers final: 18 residues processed: 98 average time/residue: 0.2271 time to fit residues: 26.4689 Evaluate side-chains 96 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 74 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 392 PHE Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 408 ARG Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 42 optimal weight: 0.0770 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 HIS ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4231 Z= 0.213 Angle : 0.605 7.351 5748 Z= 0.311 Chirality : 0.044 0.144 639 Planarity : 0.004 0.027 735 Dihedral : 4.730 21.952 646 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.29 % Allowed : 32.96 % Favored : 62.75 % 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: -3.39 (0.35), residues: 499 helix: -3.75 (0.64), residues: 24 sheet: -2.51 (0.35), residues: 185 loop : -1.91 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 436 HIS 0.009 0.001 HIS B 30 PHE 0.016 0.001 PHE F 400 TYR 0.020 0.001 TYR F 369 ARG 0.004 0.001 ARG F 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 0.504 Fit side-chains REVERT: A 91 TYR cc_start: 0.9125 (t80) cc_final: 0.8811 (t80) REVERT: A 129 LYS cc_start: 0.7426 (ttpt) cc_final: 0.7158 (tttt) REVERT: A 296 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7917 (tp) REVERT: B 19 ARG cc_start: 0.6945 (OUTLIER) cc_final: 0.6686 (mtt180) REVERT: B 20 LEU cc_start: 0.8839 (mm) cc_final: 0.8533 (mm) REVERT: F 417 LYS cc_start: 0.8136 (ttmt) cc_final: 0.7910 (ttpp) REVERT: F 465 GLU cc_start: 0.8373 (tt0) cc_final: 0.8039 (tt0) REVERT: F 498 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7839 (mm-40) outliers start: 19 outliers final: 17 residues processed: 90 average time/residue: 0.2378 time to fit residues: 25.2825 Evaluate side-chains 92 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 73 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 392 PHE Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 408 ARG Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 0.1980 chunk 49 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN B 30 HIS ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4231 Z= 0.186 Angle : 0.586 7.239 5748 Z= 0.300 Chirality : 0.044 0.143 639 Planarity : 0.003 0.026 735 Dihedral : 4.499 21.057 646 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.97 % Allowed : 32.51 % Favored : 62.53 % 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: -3.31 (0.35), residues: 499 helix: -3.53 (0.73), residues: 24 sheet: -2.44 (0.35), residues: 185 loop : -1.88 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 436 HIS 0.007 0.001 HIS B 30 PHE 0.014 0.001 PHE F 400 TYR 0.019 0.001 TYR F 369 ARG 0.004 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 77 time to evaluate : 0.486 Fit side-chains REVERT: A 129 LYS cc_start: 0.7355 (ttpt) cc_final: 0.7131 (tttt) REVERT: A 229 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6933 (mm) REVERT: B 19 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.6695 (mtt180) REVERT: B 20 LEU cc_start: 0.8808 (mm) cc_final: 0.8516 (mm) REVERT: F 417 LYS cc_start: 0.8232 (ttmt) cc_final: 0.7938 (ttpp) REVERT: F 465 GLU cc_start: 0.8329 (tt0) cc_final: 0.8033 (tt0) REVERT: F 498 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7827 (mm-40) outliers start: 22 outliers final: 19 residues processed: 96 average time/residue: 0.2149 time to fit residues: 24.7172 Evaluate side-chains 97 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 76 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 392 PHE Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 408 ARG Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 42 optimal weight: 0.0870 chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 414 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4231 Z= 0.185 Angle : 0.596 7.498 5748 Z= 0.305 Chirality : 0.044 0.172 639 Planarity : 0.003 0.028 735 Dihedral : 4.460 21.748 646 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 4.29 % Allowed : 32.28 % Favored : 63.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.35), residues: 499 helix: -3.62 (0.70), residues: 24 sheet: -2.40 (0.35), residues: 185 loop : -1.87 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 436 HIS 0.001 0.000 HIS B 112 PHE 0.014 0.001 PHE F 400 TYR 0.019 0.001 TYR F 369 ARG 0.005 0.001 ARG A 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 91 TYR cc_start: 0.9073 (t80) cc_final: 0.8770 (t80) REVERT: A 129 LYS cc_start: 0.7362 (ttpt) cc_final: 0.7129 (tttt) REVERT: A 229 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6917 (mm) REVERT: A 296 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7850 (tp) REVERT: B 19 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.6671 (mtt180) REVERT: B 20 LEU cc_start: 0.8800 (mm) cc_final: 0.8501 (mm) REVERT: F 417 LYS cc_start: 0.8204 (ttmt) cc_final: 0.7934 (ttpp) REVERT: F 465 GLU cc_start: 0.8295 (tt0) cc_final: 0.7995 (tt0) REVERT: F 498 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7813 (mm-40) outliers start: 19 outliers final: 16 residues processed: 96 average time/residue: 0.2291 time to fit residues: 26.0093 Evaluate side-chains 94 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 392 PHE Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 408 ARG Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.9980 chunk 5 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 HIS ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.153526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.124362 restraints weight = 6354.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.126718 restraints weight = 3921.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.127955 restraints weight = 3464.902| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4231 Z= 0.213 Angle : 0.605 7.288 5748 Z= 0.311 Chirality : 0.045 0.181 639 Planarity : 0.003 0.028 735 Dihedral : 4.544 21.334 646 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.74 % Allowed : 31.15 % Favored : 64.11 % 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: -3.27 (0.35), residues: 499 helix: -3.65 (0.70), residues: 24 sheet: -2.41 (0.35), residues: 180 loop : -1.87 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 436 HIS 0.007 0.001 HIS B 30 PHE 0.016 0.001 PHE F 400 TYR 0.018 0.001 TYR F 369 ARG 0.005 0.001 ARG A 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1731.13 seconds wall clock time: 32 minutes 24.19 seconds (1944.19 seconds total)