Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 02:34:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrp_33416/04_2023/7xrp_33416.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrp_33416/04_2023/7xrp_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_33416/04_2023/7xrp_33416.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrp_33416/04_2023/7xrp_33416.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrp_33416/04_2023/7xrp_33416.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrp_33416/04_2023/7xrp_33416.pdb" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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 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 chiralities: 1 Time building chain proxies: 2.71, per 1000 atoms: 0.66 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: 1.51 Conformation dependent library (CDL) restraints added in 715.1 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: 0.27 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: 1.21 Time building geometry restraints manager: 1.66 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: 2135 17.34 - 34.67: 241 34.67 - 52.01: 45 52.01 - 69.35: 5 69.35 - 86.68: 4 Dihedral angle restraints: 2430 sinusoidal: 938 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 2427 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: 6.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 27.100 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.280 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.290 ------------------------------------------------------------------------------- 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 : 14.630 86.684 1463 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 % 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 *********************** 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 : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 129 average time/residue: 0.2518 time to fit residues: 37.6518 Evaluate side-chains 88 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.501 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6663 ------------------------------------------------------------------------------- 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: 0.8980 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 39 GLN B 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2382 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= 0.307 Angle : 0.722 7.806 5748 Z= 0.375 Chirality : 0.046 0.161 639 Planarity : 0.005 0.034 735 Dihedral : 5.797 29.693 562 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer Outliers : 4.74 % 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: -4.09 (0.32), residues: 499 helix: -4.69 (0.34), residues: 30 sheet: -2.79 (0.35), residues: 171 loop : -2.49 (0.32), residues: 298 *********************** 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 125 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 0.540 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 117 average time/residue: 0.2479 time to fit residues: 33.8819 Evaluate side-chains 94 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 0.503 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0859 time to fit residues: 1.9910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 0.0370 chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 39 GLN B 74 ASN ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 4231 Z= 0.190 Angle : 0.610 5.725 5748 Z= 0.320 Chirality : 0.044 0.157 639 Planarity : 0.004 0.040 735 Dihedral : 5.032 24.646 562 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer Outliers : 2.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.33), residues: 499 helix: -4.36 (0.46), residues: 30 sheet: -2.57 (0.34), residues: 178 loop : -2.31 (0.34), residues: 291 *********************** 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 107 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.462 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 102 average time/residue: 0.2232 time to fit residues: 26.9412 Evaluate side-chains 80 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.447 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1494 time to fit residues: 1.3381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 0.0170 chunk 43 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- 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 39 GLN B 113 ASN ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3328 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= 0.227 Angle : 0.638 11.130 5748 Z= 0.325 Chirality : 0.044 0.151 639 Planarity : 0.004 0.038 735 Dihedral : 5.001 22.851 562 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer Outliers : 2.26 % 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: -3.64 (0.34), residues: 499 helix: -4.25 (0.47), residues: 30 sheet: -2.51 (0.34), residues: 186 loop : -2.11 (0.35), residues: 283 *********************** 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 94 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.511 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 91 average time/residue: 0.2319 time to fit residues: 25.0393 Evaluate side-chains 86 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 0.462 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0490 time to fit residues: 1.1735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN F 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 4231 Z= 0.255 Angle : 0.624 9.157 5748 Z= 0.320 Chirality : 0.044 0.152 639 Planarity : 0.004 0.031 735 Dihedral : 4.985 22.495 562 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer Outliers : 1.35 % 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: -3.50 (0.35), residues: 499 helix: -4.11 (0.48), residues: 30 sheet: -2.43 (0.35), residues: 185 loop : -2.01 (0.36), residues: 284 *********************** 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 89 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.496 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 88 average time/residue: 0.2531 time to fit residues: 26.3958 Evaluate side-chains 78 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.508 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2653 time to fit residues: 1.2743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3574 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= 0.299 Angle : 0.643 9.105 5748 Z= 0.330 Chirality : 0.045 0.149 639 Planarity : 0.004 0.031 735 Dihedral : 5.107 22.800 562 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer Outliers : 1.81 % 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: -3.57 (0.35), residues: 499 helix: -4.16 (0.46), residues: 30 sheet: -2.52 (0.35), residues: 185 loop : -2.02 (0.36), residues: 284 *********************** 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 88 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.498 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 86 average time/residue: 0.2418 time to fit residues: 24.5792 Evaluate side-chains 82 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 0.504 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1067 time to fit residues: 1.6706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.3980 chunk 40 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 19 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 0.1980 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 414 GLN F 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 4231 Z= 0.180 Angle : 0.577 7.717 5748 Z= 0.295 Chirality : 0.043 0.149 639 Planarity : 0.004 0.032 735 Dihedral : 4.602 21.561 562 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer Outliers : 1.13 % 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: -3.33 (0.35), residues: 499 helix: -3.93 (0.58), residues: 24 sheet: -2.37 (0.35), residues: 185 loop : -1.92 (0.35), residues: 290 *********************** 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 88 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.453 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 88 average time/residue: 0.2303 time to fit residues: 24.3671 Evaluate side-chains 77 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.499 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0449 time to fit residues: 0.9838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 0.0570 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 4231 Z= 0.217 Angle : 0.609 7.219 5748 Z= 0.309 Chirality : 0.044 0.146 639 Planarity : 0.004 0.032 735 Dihedral : 4.637 21.431 562 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer Outliers : 0.45 % 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: -3.32 (0.35), residues: 499 helix: -3.86 (0.62), residues: 24 sheet: -2.38 (0.35), residues: 185 loop : -1.90 (0.36), residues: 290 *********************** 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 82 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 0.499 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 80 average time/residue: 0.1979 time to fit residues: 19.3501 Evaluate side-chains 77 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 0.443 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0526 time to fit residues: 0.7675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 chunk 44 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 0.0050 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 39 optimal weight: 0.2980 overall best weight: 0.3794 ------------------------------------------------------------------------------- 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: 0.7783 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 4231 Z= 0.174 Angle : 0.600 7.403 5748 Z= 0.303 Chirality : 0.044 0.144 639 Planarity : 0.004 0.033 735 Dihedral : 4.447 21.571 562 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 0.23 % 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: -3.19 (0.35), residues: 499 helix: -3.54 (0.73), residues: 24 sheet: -2.26 (0.35), residues: 186 loop : -1.86 (0.36), residues: 289 *********************** 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 81 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.525 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.2179 time to fit residues: 21.1081 Evaluate side-chains 75 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.489 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 0.0370 chunk 24 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.0030 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 overall best weight: 0.3868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 4231 Z= 0.176 Angle : 0.606 7.577 5748 Z= 0.305 Chirality : 0.044 0.155 639 Planarity : 0.004 0.033 735 Dihedral : 4.414 21.684 562 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer Outliers : 0.23 % 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: -3.13 (0.35), residues: 499 helix: -3.45 (0.75), residues: 24 sheet: -2.20 (0.35), residues: 186 loop : -1.84 (0.36), residues: 289 ********************** 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 80 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.450 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 80 average time/residue: 0.2085 time to fit residues: 20.2612 Evaluate side-chains 73 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.496 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0418 time to fit residues: 0.7448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.155646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.126058 restraints weight = 6359.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.128836 restraints weight = 3915.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.129857 restraints weight = 3401.949| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4224 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= 0.212 Angle : 0.637 7.275 5748 Z= 0.323 Chirality : 0.045 0.160 639 Planarity : 0.004 0.032 735 Dihedral : 4.531 21.617 562 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 0.68 % 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: -3.11 (0.36), residues: 499 helix: -3.45 (0.72), residues: 24 sheet: -2.20 (0.36), residues: 185 loop : -1.81 (0.36), residues: 290 =============================================================================== Job complete usr+sys time: 1673.90 seconds wall clock time: 30 minutes 32.43 seconds (1832.43 seconds total)