Starting phenix.real_space_refine on Fri Apr 5 17:47:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfi_37492/04_2024/8wfi_37492.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfi_37492/04_2024/8wfi_37492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfi_37492/04_2024/8wfi_37492.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfi_37492/04_2024/8wfi_37492.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfi_37492/04_2024/8wfi_37492.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfi_37492/04_2024/8wfi_37492.pdb" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.067 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: 6 Type Number sf(0) Gaussians S 35 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2877 2.51 5 N 676 2.21 5 O 756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "A ASP 432": "OD1" <-> "OD2" Residue "A ASP 582": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 4347 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4302 Classifications: {'peptide': 542} Link IDs: {'PTRANS': 25, 'TRANS': 516} Chain breaks: 1 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Unusual residues: {' CL': 1, ' NA': 2} Classifications: {'undetermined': 3, 'water': 37} Link IDs: {None: 39} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY A 701 " occ=0.00 ... (3 atoms not shown) pdb=" OXT GLY A 701 " occ=0.00 Time building chain proxies: 2.96, per 1000 atoms: 0.68 Number of scatterers: 4347 At special positions: 0 Unit cell: (75.65, 65.45, 93.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 35 16.00 Na 2 11.00 O 756 8.00 N 676 7.00 C 2877 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 175 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 782.3 milliseconds 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 988 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 78.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 51 through 64 removed outlier: 3.594A pdb=" N PHE A 55 " --> pdb=" O ASN A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.054A pdb=" N VAL A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 79 removed outlier: 4.124A pdb=" N TYR A 74 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 83 Processing helix chain 'A' and resid 84 through 95 Processing helix chain 'A' and resid 95 through 111 removed outlier: 3.942A pdb=" N ALA A 110 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.719A pdb=" N TRP A 118 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A 119 " --> pdb=" O GLY A 116 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 120 " --> pdb=" O VAL A 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 115 through 120' Processing helix chain 'A' and resid 121 through 124 Processing helix chain 'A' and resid 125 through 156 removed outlier: 3.649A pdb=" N TYR A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASN A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 218 Processing helix chain 'A' and resid 233 through 253 Processing helix chain 'A' and resid 254 through 257 Processing helix chain 'A' and resid 258 through 266 removed outlier: 3.873A pdb=" N VAL A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 281 removed outlier: 3.587A pdb=" N VAL A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.569A pdb=" N GLY A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.897A pdb=" N TRP A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 330 removed outlier: 3.721A pdb=" N THR A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 372 removed outlier: 3.929A pdb=" N ASP A 341 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 342 " --> pdb=" O CYS A 338 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE A 363 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 395 removed outlier: 4.555A pdb=" N TYR A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Proline residue: A 391 - end of helix Processing helix chain 'A' and resid 399 through 435 removed outlier: 3.804A pdb=" N TRP A 403 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 removed outlier: 3.692A pdb=" N LEU A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 459 Processing helix chain 'A' and resid 460 through 463 removed outlier: 3.777A pdb=" N SER A 463 " --> pdb=" O PRO A 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 460 through 463' Processing helix chain 'A' and resid 465 through 477 removed outlier: 3.676A pdb=" N TRP A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 496 Processing helix chain 'A' and resid 498 through 511 Processing helix chain 'A' and resid 515 through 540 removed outlier: 5.656A pdb=" N SER A 526 " --> pdb=" O TRP A 522 " (cutoff:3.500A) Proline residue: A 527 - end of helix Processing helix chain 'A' and resid 552 through 568 removed outlier: 4.272A pdb=" N SER A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL A 567 " --> pdb=" O ALA A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 579 Processing helix chain 'A' and resid 585 through 595 removed outlier: 3.534A pdb=" N LYS A 595 " --> pdb=" O LYS A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 608 Processing sheet with id=AA1, first strand: chain 'A' and resid 545 through 546 273 hydrogen bonds defined for protein. 801 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: 1.17 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1269 1.34 - 1.46: 1078 1.46 - 1.58: 2045 1.58 - 1.69: 0 1.69 - 1.81: 53 Bond restraints: 4445 Sorted by residual: bond pdb=" N GLY A 701 " pdb=" CA GLY A 701 " ideal model delta sigma weight residual 1.451 1.477 -0.026 1.60e-02 3.91e+03 2.62e+00 bond pdb=" N GLY A 610 " pdb=" CA GLY A 610 " ideal model delta sigma weight residual 1.449 1.468 -0.018 1.45e-02 4.76e+03 1.61e+00 bond pdb=" C TYR A 141 " pdb=" O TYR A 141 " ideal model delta sigma weight residual 1.236 1.247 -0.011 1.28e-02 6.10e+03 6.97e-01 bond pdb=" CA PHE A 268 " pdb=" C PHE A 268 " ideal model delta sigma weight residual 1.522 1.531 -0.009 1.26e-02 6.30e+03 5.51e-01 bond pdb=" CA ILE A 97 " pdb=" C ILE A 97 " ideal model delta sigma weight residual 1.520 1.526 -0.007 8.80e-03 1.29e+04 5.46e-01 ... (remaining 4440 not shown) Histogram of bond angle deviations from ideal: 100.56 - 107.26: 164 107.26 - 113.96: 2353 113.96 - 120.67: 1978 120.67 - 127.37: 1507 127.37 - 134.08: 60 Bond angle restraints: 6062 Sorted by residual: angle pdb=" C THR A 267 " pdb=" N PHE A 268 " pdb=" CA PHE A 268 " ideal model delta sigma weight residual 120.09 123.98 -3.89 1.25e+00 6.40e-01 9.69e+00 angle pdb=" O GLY A 701 " pdb=" C GLY A 701 " pdb=" OXT GLY A 701 " ideal model delta sigma weight residual 118.00 125.77 -7.77 3.00e+00 1.11e-01 6.70e+00 angle pdb=" C PRO A 73 " pdb=" N TYR A 74 " pdb=" CA TYR A 74 " ideal model delta sigma weight residual 121.14 117.03 4.11 1.75e+00 3.27e-01 5.53e+00 angle pdb=" C PRO A 398 " pdb=" N ILE A 399 " pdb=" CA ILE A 399 " ideal model delta sigma weight residual 121.97 125.99 -4.02 1.80e+00 3.09e-01 4.99e+00 angle pdb=" CA TYR A 74 " pdb=" CB TYR A 74 " pdb=" CG TYR A 74 " ideal model delta sigma weight residual 113.90 117.82 -3.92 1.80e+00 3.09e-01 4.74e+00 ... (remaining 6057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 2274 16.39 - 32.77: 191 32.77 - 49.16: 30 49.16 - 65.54: 6 65.54 - 81.93: 3 Dihedral angle restraints: 2504 sinusoidal: 942 harmonic: 1562 Sorted by residual: dihedral pdb=" CA PHE A 524 " pdb=" C PHE A 524 " pdb=" N VAL A 525 " pdb=" CA VAL A 525 " ideal model delta harmonic sigma weight residual -180.00 -157.65 -22.35 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA TRP A 118 " pdb=" C TRP A 118 " pdb=" N ARG A 119 " pdb=" CA ARG A 119 " ideal model delta harmonic sigma weight residual 180.00 163.39 16.61 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CB MET A 102 " pdb=" CG MET A 102 " pdb=" SD MET A 102 " pdb=" CE MET A 102 " ideal model delta sinusoidal sigma weight residual -60.00 -111.29 51.29 3 1.50e+01 4.44e-03 9.00e+00 ... (remaining 2501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 378 0.026 - 0.051: 174 0.051 - 0.077: 80 0.077 - 0.102: 29 0.102 - 0.128: 8 Chirality restraints: 669 Sorted by residual: chirality pdb=" CA PRO A 73 " pdb=" N PRO A 73 " pdb=" C PRO A 73 " pdb=" CB PRO A 73 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA VAL A 160 " pdb=" N VAL A 160 " pdb=" C VAL A 160 " pdb=" CB VAL A 160 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.33e-01 chirality pdb=" CA PRO A 122 " pdb=" N PRO A 122 " pdb=" C PRO A 122 " pdb=" CB PRO A 122 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.24e-01 ... (remaining 666 not shown) Planarity restraints: 744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 106 " -0.020 2.00e-02 2.50e+03 1.97e-02 6.77e+00 pdb=" CG PHE A 106 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 106 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 106 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 106 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 106 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 106 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 521 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.52e+00 pdb=" C CYS A 521 " 0.032 2.00e-02 2.50e+03 pdb=" O CYS A 521 " -0.012 2.00e-02 2.50e+03 pdb=" N TRP A 522 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 355 " 0.013 2.00e-02 2.50e+03 9.92e-03 1.97e+00 pdb=" CG TYR A 355 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 355 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 355 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 355 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 355 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 355 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 355 " 0.002 2.00e-02 2.50e+03 ... (remaining 741 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1148 2.80 - 3.33: 3991 3.33 - 3.85: 7270 3.85 - 4.38: 8505 4.38 - 4.90: 14699 Nonbonded interactions: 35613 Sorted by model distance: nonbonded pdb=" OG SER A 597 " pdb=" OD1 ASP A 599 " model vdw 2.278 2.440 nonbonded pdb=" O PRO A 602 " pdb=" NH2 ARG A 608 " model vdw 2.278 2.520 nonbonded pdb=" O SER A 479 " pdb=" O HOH A 801 " model vdw 2.280 2.440 nonbonded pdb=" O TYR A 476 " pdb=" O HOH A 801 " model vdw 2.307 2.440 nonbonded pdb=" OE1 GLN A 52 " pdb=" NH2 ARG A 340 " model vdw 2.372 2.520 ... (remaining 35608 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.010 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.090 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 0.002 0.029 4445 Z= 0.160 Angle : 0.568 7.766 6062 Z= 0.305 Chirality : 0.038 0.128 669 Planarity : 0.004 0.033 744 Dihedral : 12.583 81.926 1513 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.36), residues: 538 helix: 2.12 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -1.16 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 215 HIS 0.002 0.001 HIS A 499 PHE 0.045 0.002 PHE A 106 TYR 0.024 0.002 TYR A 355 ARG 0.006 0.001 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.471 Fit side-chains REVERT: A 212 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7561 (tp30) REVERT: A 260 LYS cc_start: 0.7546 (mttm) cc_final: 0.6799 (mmpt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 1.2064 time to fit residues: 96.4528 Evaluate side-chains 65 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.0870 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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: 0.8035 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4445 Z= 0.183 Angle : 0.548 6.192 6062 Z= 0.293 Chirality : 0.039 0.128 669 Planarity : 0.005 0.039 744 Dihedral : 4.011 22.584 594 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.54 % Allowed : 7.69 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.36), residues: 538 helix: 2.12 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.29 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 215 HIS 0.004 0.001 HIS A 499 PHE 0.040 0.002 PHE A 106 TYR 0.024 0.002 TYR A 74 ARG 0.002 0.000 ARG A 608 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.508 Fit side-chains REVERT: A 507 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: A 606 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7165 (pm20) outliers start: 7 outliers final: 2 residues processed: 63 average time/residue: 1.2285 time to fit residues: 80.5833 Evaluate side-chains 63 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 606 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4445 Z= 0.182 Angle : 0.546 6.335 6062 Z= 0.291 Chirality : 0.039 0.129 669 Planarity : 0.005 0.043 744 Dihedral : 3.994 23.042 594 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.98 % Allowed : 8.57 % Favored : 89.45 % 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: 1.75 (0.36), residues: 538 helix: 2.19 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.28 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 215 HIS 0.005 0.001 HIS A 499 PHE 0.034 0.002 PHE A 106 TYR 0.023 0.002 TYR A 74 ARG 0.002 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.495 Fit side-chains REVERT: A 507 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7833 (tt0) REVERT: A 550 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.6561 (mm-40) REVERT: A 606 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7154 (pm20) outliers start: 9 outliers final: 3 residues processed: 61 average time/residue: 1.1462 time to fit residues: 72.8783 Evaluate side-chains 63 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 606 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 46 optimal weight: 0.3980 chunk 14 optimal weight: 0.0570 chunk 43 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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: 0.8028 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4445 Z= 0.160 Angle : 0.515 6.350 6062 Z= 0.274 Chirality : 0.038 0.126 669 Planarity : 0.004 0.040 744 Dihedral : 3.881 22.970 594 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.76 % Allowed : 10.11 % Favored : 88.13 % 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: 1.94 (0.37), residues: 538 helix: 2.34 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.24 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 215 HIS 0.004 0.001 HIS A 499 PHE 0.021 0.001 PHE A 106 TYR 0.021 0.002 TYR A 74 ARG 0.002 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.773 Fit side-chains REVERT: A 402 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6563 (tp) REVERT: A 507 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: A 550 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.6559 (mm-40) outliers start: 8 outliers final: 2 residues processed: 60 average time/residue: 1.2273 time to fit residues: 76.7672 Evaluate side-chains 62 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 550 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 36 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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: 0.8039 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4445 Z= 0.169 Angle : 0.525 6.306 6062 Z= 0.279 Chirality : 0.039 0.128 669 Planarity : 0.005 0.041 744 Dihedral : 3.907 22.972 594 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.98 % Allowed : 10.77 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.37), residues: 538 helix: 2.34 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.23 (0.47), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 215 HIS 0.004 0.001 HIS A 499 PHE 0.019 0.002 PHE A 106 TYR 0.021 0.002 TYR A 74 ARG 0.002 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.499 Fit side-chains REVERT: A 71 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7700 (ttt-90) REVERT: A 507 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: A 550 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.6605 (mm-40) REVERT: A 606 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.6935 (pm20) outliers start: 9 outliers final: 5 residues processed: 62 average time/residue: 1.2072 time to fit residues: 77.9200 Evaluate side-chains 66 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 606 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.0040 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 50 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 overall best weight: 0.3992 ------------------------------------------------------------------------------- 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: 0.7999 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4445 Z= 0.140 Angle : 0.488 6.196 6062 Z= 0.257 Chirality : 0.038 0.117 669 Planarity : 0.004 0.037 744 Dihedral : 3.741 22.771 594 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.98 % Allowed : 10.99 % Favored : 87.03 % 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: 2.16 (0.37), residues: 538 helix: 2.51 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.16 (0.47), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 215 HIS 0.003 0.001 HIS A 499 PHE 0.012 0.001 PHE A 106 TYR 0.018 0.001 TYR A 74 ARG 0.001 0.000 ARG A 611 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 402 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6445 (tp) REVERT: A 507 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: A 550 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.6564 (mm-40) REVERT: A 606 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.6928 (pm20) outliers start: 9 outliers final: 4 residues processed: 65 average time/residue: 1.1689 time to fit residues: 79.1771 Evaluate side-chains 66 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 606 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.0980 chunk 43 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4445 Z= 0.158 Angle : 0.511 6.161 6062 Z= 0.270 Chirality : 0.038 0.123 669 Planarity : 0.004 0.039 744 Dihedral : 3.809 22.786 594 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.42 % Allowed : 10.33 % Favored : 87.25 % 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: 2.10 (0.37), residues: 538 helix: 2.46 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.18 (0.47), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 215 HIS 0.004 0.001 HIS A 499 PHE 0.014 0.001 PHE A 106 TYR 0.020 0.002 TYR A 74 ARG 0.002 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 507 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.7845 (tt0) REVERT: A 550 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.6576 (mm-40) REVERT: A 606 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.6930 (pm20) outliers start: 11 outliers final: 6 residues processed: 64 average time/residue: 1.1208 time to fit residues: 74.7138 Evaluate side-chains 67 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 606 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.8045 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4445 Z= 0.178 Angle : 0.529 6.280 6062 Z= 0.282 Chirality : 0.039 0.128 669 Planarity : 0.005 0.041 744 Dihedral : 3.918 23.065 594 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.20 % Allowed : 10.55 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.37), residues: 538 helix: 2.37 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.19 (0.47), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 215 HIS 0.005 0.001 HIS A 499 PHE 0.015 0.002 PHE A 106 TYR 0.022 0.002 TYR A 74 ARG 0.002 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 507 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7887 (tt0) REVERT: A 550 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.6615 (mm-40) REVERT: A 606 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.6937 (pm20) outliers start: 10 outliers final: 6 residues processed: 63 average time/residue: 1.1399 time to fit residues: 74.7939 Evaluate side-chains 66 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 606 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 0.1980 chunk 31 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8049 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4445 Z= 0.184 Angle : 0.541 6.330 6062 Z= 0.287 Chirality : 0.039 0.129 669 Planarity : 0.005 0.041 744 Dihedral : 3.951 23.113 594 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.64 % Allowed : 9.89 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.37), residues: 538 helix: 2.31 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.21 (0.47), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 215 HIS 0.005 0.001 HIS A 499 PHE 0.016 0.002 PHE A 106 TYR 0.022 0.002 TYR A 74 ARG 0.002 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.494 Fit side-chains REVERT: A 71 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7740 (ttt-90) REVERT: A 507 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: A 550 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.6623 (mm-40) REVERT: A 606 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.6936 (pm20) outliers start: 12 outliers final: 7 residues processed: 62 average time/residue: 1.1236 time to fit residues: 72.6220 Evaluate side-chains 66 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 606 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 13 optimal weight: 0.0670 chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.5076 ------------------------------------------------------------------------------- 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: 0.8021 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4445 Z= 0.157 Angle : 0.507 6.231 6062 Z= 0.269 Chirality : 0.038 0.120 669 Planarity : 0.004 0.039 744 Dihedral : 3.833 22.969 594 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.20 % Allowed : 10.55 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.37), residues: 538 helix: 2.42 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.17 (0.47), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 215 HIS 0.004 0.001 HIS A 499 PHE 0.013 0.001 PHE A 106 TYR 0.019 0.001 TYR A 74 ARG 0.001 0.000 ARG A 233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 507 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: A 550 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.6601 (mm-40) REVERT: A 606 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.6925 (pm20) outliers start: 10 outliers final: 6 residues processed: 61 average time/residue: 1.1725 time to fit residues: 74.5657 Evaluate side-chains 66 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 606 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.155029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.139654 restraints weight = 4208.143| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 0.87 r_work: 0.3447 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4445 Z= 0.202 Angle : 0.559 6.332 6062 Z= 0.298 Chirality : 0.040 0.122 669 Planarity : 0.005 0.042 744 Dihedral : 4.009 23.122 594 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.42 % Allowed : 10.11 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.37), residues: 538 helix: 2.27 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.22 (0.47), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 215 HIS 0.005 0.001 HIS A 499 PHE 0.017 0.002 PHE A 106 TYR 0.014 0.002 TYR A 74 ARG 0.003 0.000 ARG A 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1989.91 seconds wall clock time: 36 minutes 2.32 seconds (2162.32 seconds total)