Starting phenix.real_space_refine on Thu Dec 7 19:57:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrp_33416/12_2023/7xrp_33416.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrp_33416/12_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_33416/12_2023/7xrp_33416.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrp_33416/12_2023/7xrp_33416.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrp_33416/12_2023/7xrp_33416.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrp_33416/12_2023/7xrp_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-1.21rc1-5172/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: 2.73, 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: 1.50 Conformation dependent library (CDL) restraints added in 882.6 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: 0.47 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: 1.26 Time building geometry restraints manager: 1.64 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: 6.470 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: 0.060 Process input model: 15.970 Find NCS groups from input model: 0.120 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.590 ------------------------------------------------------------------------------- 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 : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 129 average time/residue: 0.2530 time to fit residues: 37.8555 Evaluate side-chains 88 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.368 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6315 ------------------------------------------------------------------------------- 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: 0.7902 moved from start: 0.2456 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= 0.306 Angle : 0.714 7.659 5748 Z= 0.372 Chirality : 0.046 0.166 639 Planarity : 0.005 0.038 735 Dihedral : 6.856 57.986 646 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 4.97 % Allowed : 21.22 % Favored : 73.81 % 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: -4.10 (0.33), residues: 499 helix: -4.67 (0.35), residues: 30 sheet: -2.74 (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 0.007 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 125 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 0.344 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 117 average time/residue: 0.1791 time to fit residues: 24.4743 Evaluate side-chains 93 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 0.368 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0615 time to fit residues: 1.3735 ------------------------------------------------------------------------------- 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: 0.0980 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7843 moved from start: 0.3105 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= 0.210 Angle : 0.619 6.092 5748 Z= 0.326 Chirality : 0.044 0.155 639 Planarity : 0.004 0.045 735 Dihedral : 6.327 59.363 646 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.16 % Allowed : 24.38 % Favored : 72.46 % 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: -3.80 (0.34), residues: 499 helix: -4.37 (0.46), residues: 30 sheet: -2.57 (0.34), residues: 180 loop : -2.28 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 353 HIS 0.005 0.001 HIS B 30 PHE 0.026 0.002 PHE A 275 TYR 0.022 0.001 TYR A 170 ARG 0.010 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 112 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 0.490 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 106 average time/residue: 0.2219 time to fit residues: 27.9461 Evaluate side-chains 88 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.491 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1131 time to fit residues: 1.6742 ------------------------------------------------------------------------------- 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: 3.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 45 optimal weight: 0.0060 chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 0.0670 overall best weight: 0.5136 ------------------------------------------------------------------------------- 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: 0.7819 moved from start: 0.3419 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= 0.193 Angle : 0.615 10.914 5748 Z= 0.313 Chirality : 0.044 0.152 639 Planarity : 0.004 0.036 735 Dihedral : 5.323 37.895 646 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.35 % Allowed : 27.09 % Favored : 71.56 % 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: -3.53 (0.35), residues: 499 helix: -4.60 (0.34), residues: 24 sheet: -2.50 (0.34), residues: 186 loop : -2.01 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 436 HIS 0.005 0.001 HIS B 30 PHE 0.018 0.001 PHE F 338 TYR 0.017 0.001 TYR F 369 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 90 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.480 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 88 average time/residue: 0.2331 time to fit residues: 24.5109 Evaluate side-chains 80 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.481 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0462 time to fit residues: 0.8575 ------------------------------------------------------------------------------- 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: 2.9990 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 0.0370 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- 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: 0.7920 moved from start: 0.3528 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= 0.349 Angle : 0.677 9.032 5748 Z= 0.350 Chirality : 0.046 0.150 639 Planarity : 0.004 0.032 735 Dihedral : 5.510 24.423 646 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 2.93 % Allowed : 30.02 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.35), residues: 499 helix: -4.26 (0.45), residues: 30 sheet: -2.52 (0.34), residues: 186 loop : -2.05 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 436 HIS 0.002 0.001 HIS B 30 PHE 0.021 0.002 PHE A 275 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 95 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.506 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 92 average time/residue: 0.2397 time to fit residues: 26.2659 Evaluate side-chains 89 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.514 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0483 time to fit residues: 1.3682 ------------------------------------------------------------------------------- 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: 1.9990 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3644 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= 0.315 Angle : 0.670 11.100 5748 Z= 0.343 Chirality : 0.046 0.146 639 Planarity : 0.004 0.032 735 Dihedral : 5.377 23.619 646 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 2.03 % Allowed : 31.38 % Favored : 66.59 % 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: -3.65 (0.35), residues: 499 helix: -4.16 (0.46), residues: 30 sheet: -2.61 (0.35), residues: 181 loop : -2.07 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 436 HIS 0.001 0.000 HIS B 30 PHE 0.024 0.002 PHE F 400 TYR 0.023 0.002 TYR F 369 ARG 0.006 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 89 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.472 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 87 average time/residue: 0.2332 time to fit residues: 24.0732 Evaluate side-chains 80 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.470 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1063 time to fit residues: 1.7635 ------------------------------------------------------------------------------- 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: 2.9990 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.0470 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3781 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= 0.213 Angle : 0.604 7.510 5748 Z= 0.310 Chirality : 0.044 0.144 639 Planarity : 0.004 0.033 735 Dihedral : 4.908 22.791 646 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.90 % Allowed : 32.51 % Favored : 66.59 % 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: -3.52 (0.35), residues: 499 helix: -3.83 (0.54), residues: 30 sheet: -2.57 (0.35), residues: 180 loop : -1.99 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 436 HIS 0.001 0.000 HIS A 49 PHE 0.017 0.001 PHE F 400 TYR 0.023 0.001 TYR F 369 ARG 0.006 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 87 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 0.489 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 86 average time/residue: 0.2250 time to fit residues: 23.3796 Evaluate side-chains 74 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.492 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0458 time to fit residues: 0.7422 ------------------------------------------------------------------------------- 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: 0.6980 chunk 4 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 46 optimal weight: 0.0670 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 19 optimal weight: 0.0970 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 overall best weight: 0.3716 ------------------------------------------------------------------------------- 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** F 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3987 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 : 0.601 6.914 5748 Z= 0.308 Chirality : 0.044 0.145 639 Planarity : 0.004 0.034 735 Dihedral : 4.575 21.722 646 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.68 % Allowed : 31.38 % Favored : 67.95 % 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: -3.34 (0.35), residues: 499 helix: -3.75 (0.64), residues: 24 sheet: -2.48 (0.35), residues: 181 loop : -1.88 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 436 HIS 0.006 0.001 HIS B 30 PHE 0.013 0.001 PHE F 400 TYR 0.022 0.001 TYR F 369 ARG 0.004 0.001 ARG A 34 *********************** 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 81 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.428 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 80 average time/residue: 0.2011 time to fit residues: 19.4366 Evaluate side-chains 80 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.438 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0532 time to fit residues: 0.6634 ------------------------------------------------------------------------------- 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: 1.9990 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 0.0000 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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: 0.7813 moved from start: 0.4079 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= 0.194 Angle : 0.614 7.209 5748 Z= 0.311 Chirality : 0.044 0.146 639 Planarity : 0.004 0.034 735 Dihedral : 4.489 20.488 646 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.68 % Allowed : 31.83 % 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: -3.26 (0.35), residues: 499 helix: -3.61 (0.68), residues: 24 sheet: -2.34 (0.35), residues: 186 loop : -1.88 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 436 HIS 0.002 0.000 HIS B 30 PHE 0.017 0.001 PHE F 338 TYR 0.020 0.001 TYR F 369 ARG 0.005 0.001 ARG F 466 *********************** 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 84 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.439 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 83 average time/residue: 0.2061 time to fit residues: 20.8412 Evaluate side-chains 79 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.473 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0563 time to fit residues: 0.9224 ------------------------------------------------------------------------------- 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: 0.0670 chunk 30 optimal weight: 0.0170 chunk 24 optimal weight: 0.0770 chunk 31 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 overall best weight: 0.2914 ------------------------------------------------------------------------------- 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: 0.7761 moved from start: 0.4245 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= 0.169 Angle : 0.611 7.416 5748 Z= 0.309 Chirality : 0.044 0.164 639 Planarity : 0.004 0.034 735 Dihedral : 4.317 19.811 646 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 32.28 % Favored : 67.72 % 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: -3.01 (0.36), residues: 499 helix: -2.86 (1.04), residues: 16 sheet: -2.22 (0.35), residues: 185 loop : -1.78 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 436 HIS 0.007 0.001 HIS B 30 PHE 0.024 0.001 PHE A 238 TYR 0.021 0.001 TYR F 369 ARG 0.004 0.001 ARG F 466 ********************** 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 79 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.510 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2210 time to fit residues: 21.1090 Evaluate side-chains 71 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.460 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6734 ------------------------------------------------------------------------------- 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: 0.5980 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.154361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.124924 restraints weight = 6384.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.127581 restraints weight = 4009.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.129052 restraints weight = 3375.060| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4196 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= 0.222 Angle : 0.635 7.356 5748 Z= 0.322 Chirality : 0.044 0.159 639 Planarity : 0.004 0.033 735 Dihedral : 4.484 20.090 646 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.45 % Allowed : 32.05 % 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: -2.97 (0.36), residues: 499 helix: -2.94 (0.97), residues: 16 sheet: -2.24 (0.35), residues: 185 loop : -1.71 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 436 HIS 0.001 0.000 HIS B 30 PHE 0.025 0.002 PHE A 238 TYR 0.019 0.001 TYR F 369 ARG 0.005 0.001 ARG F 466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1678.45 seconds wall clock time: 34 minutes 58.57 seconds (2098.57 seconds total)