Starting phenix.real_space_refine on Fri Dec 27 13:46:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v0q_26948/12_2024/7v0q_26948.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v0q_26948/12_2024/7v0q_26948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v0q_26948/12_2024/7v0q_26948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v0q_26948/12_2024/7v0q_26948.map" model { file = "/net/cci-nas-00/data/ceres_data/7v0q_26948/12_2024/7v0q_26948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v0q_26948/12_2024/7v0q_26948.cif" } resolution = 2.5 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= 0.249 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 23 5.16 5 C 3282 2.51 5 N 916 2.21 5 O 1080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5301 Number of models: 1 Model: "" Number of chains: 2 Chain: "X" Number of atoms: 5174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5174 Classifications: {'peptide': 658} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 30, 'TRANS': 627} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "X" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 127 Classifications: {'water': 127} Link IDs: {None: 126} Time building chain proxies: 3.80, per 1000 atoms: 0.72 Number of scatterers: 5301 At special positions: 0 Unit cell: (98.355, 101.675, 73.04, 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 23 16.00 O 1080 8.00 N 916 7.00 C 3282 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.23 Conformation dependent library (CDL) restraints added in 617.5 milliseconds 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1234 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 10 sheets defined 21.3% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'X' and resid 13 through 21 Processing helix chain 'X' and resid 51 through 58 removed outlier: 3.570A pdb=" N ALA X 55 " --> pdb=" O ALA X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 151 through 159 Processing helix chain 'X' and resid 187 through 197 Processing helix chain 'X' and resid 201 through 206 removed outlier: 4.047A pdb=" N SER X 206 " --> pdb=" O GLU X 203 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 227 Processing helix chain 'X' and resid 247 through 258 removed outlier: 4.141A pdb=" N ILE X 251 " --> pdb=" O GLY X 247 " (cutoff:3.500A) Processing helix chain 'X' and resid 264 through 268 Processing helix chain 'X' and resid 269 through 283 removed outlier: 4.344A pdb=" N ALA X 273 " --> pdb=" O TRP X 269 " (cutoff:3.500A) Processing helix chain 'X' and resid 368 through 374 Processing helix chain 'X' and resid 381 through 389 removed outlier: 3.661A pdb=" N ILE X 389 " --> pdb=" O LEU X 385 " (cutoff:3.500A) Processing helix chain 'X' and resid 431 through 436 removed outlier: 3.914A pdb=" N TYR X 435 " --> pdb=" O ILE X 431 " (cutoff:3.500A) Processing helix chain 'X' and resid 441 through 459 Processing helix chain 'X' and resid 550 through 552 No H-bonds generated for 'chain 'X' and resid 550 through 552' Processing sheet with id=AA1, first strand: chain 'X' and resid 7 through 11 removed outlier: 6.826A pdb=" N TYR X 44 " --> pdb=" O LYS X 8 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N CYS X 10 " --> pdb=" O ILE X 42 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE X 42 " --> pdb=" O CYS X 10 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N SER X 105 " --> pdb=" O VAL X 94 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL X 94 " --> pdb=" O SER X 105 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N THR X 107 " --> pdb=" O ALA X 92 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ALA X 92 " --> pdb=" O THR X 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'X' and resid 31 through 34 removed outlier: 4.709A pdb=" N LEU X 31 " --> pdb=" O GLN X 133 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU X 130 " --> pdb=" O LEU X 121 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU X 121 " --> pdb=" O LEU X 130 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY X 132 " --> pdb=" O LEU X 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 163 through 169 Processing sheet with id=AA4, first strand: chain 'X' and resid 362 through 367 removed outlier: 3.804A pdb=" N SER X 362 " --> pdb=" O SER X 352 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR X 330 " --> pdb=" O LEU X 349 " (cutoff:3.500A) removed outlier: 11.935A pdb=" N THR X 328 " --> pdb=" O PRO X 351 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE X 326 " --> pdb=" O PHE X 292 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHE X 292 " --> pdb=" O PHE X 326 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR X 328 " --> pdb=" O THR X 290 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR X 290 " --> pdb=" O THR X 328 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR X 330 " --> pdb=" O VAL X 288 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL X 288 " --> pdb=" O THR X 330 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N CYS X 332 " --> pdb=" O ALA X 286 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA X 286 " --> pdb=" O CYS X 332 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N VAL X 288 " --> pdb=" O THR X 420 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N THR X 420 " --> pdb=" O VAL X 288 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR X 290 " --> pdb=" O ILE X 418 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE X 418 " --> pdb=" O THR X 290 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'X' and resid 303 through 309 removed outlier: 5.992A pdb=" N ILE X 304 " --> pdb=" O VAL X 394 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N TRP X 396 " --> pdb=" O ILE X 304 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLU X 306 " --> pdb=" O TRP X 396 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N CYS X 398 " --> pdb=" O GLU X 306 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR X 308 " --> pdb=" O CYS X 398 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 408 through 409 removed outlier: 6.337A pdb=" N ASP X 408 " --> pdb=" O PHE X 578 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N GLN X 580 " --> pdb=" O ASP X 408 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU X 485 " --> pdb=" O CYS X 586 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'X' and resid 408 through 409 removed outlier: 6.337A pdb=" N ASP X 408 " --> pdb=" O PHE X 578 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N GLN X 580 " --> pdb=" O ASP X 408 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS X 505 " --> pdb=" O THR X 534 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N THR X 534 " --> pdb=" O LYS X 505 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL X 507 " --> pdb=" O HIS X 532 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N HIS X 532 " --> pdb=" O VAL X 507 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU X 509 " --> pdb=" O LYS X 530 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS X 530 " --> pdb=" O LEU X 509 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE X 511 " --> pdb=" O ARG X 528 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG X 528 " --> pdb=" O ILE X 511 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL X 513 " --> pdb=" O LEU X 526 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'X' and resid 475 through 480 Processing sheet with id=AA9, first strand: chain 'X' and resid 590 through 593 Processing sheet with id=AB1, first strand: chain 'X' and resid 597 through 599 removed outlier: 6.518A pdb=" N ALA X 598 " --> pdb=" O VAL X 685 " (cutoff:3.500A) 201 hydrogen bonds defined for protein. 558 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: 1.98 Time building geometry restraints manager: 1.40 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: 1719 1.34 - 1.46: 1130 1.46 - 1.58: 2401 1.58 - 1.70: 0 1.70 - 1.82: 31 Bond restraints: 5281 Sorted by residual: bond pdb=" N GLY X 489 " pdb=" CA GLY X 489 " ideal model delta sigma weight residual 1.449 1.436 0.013 1.45e-02 4.76e+03 8.03e-01 bond pdb=" CA ILE X 81 " pdb=" CB ILE X 81 " ideal model delta sigma weight residual 1.531 1.541 -0.009 1.16e-02 7.43e+03 6.56e-01 bond pdb=" CA SER X 473 " pdb=" C SER X 473 " ideal model delta sigma weight residual 1.525 1.542 -0.017 2.10e-02 2.27e+03 6.46e-01 bond pdb=" C ASP X 344 " pdb=" N GLY X 345 " ideal model delta sigma weight residual 1.335 1.329 0.006 7.50e-03 1.78e+04 6.43e-01 bond pdb=" CB GLU X 144 " pdb=" CG GLU X 144 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.31e-01 ... (remaining 5276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 7041 1.83 - 3.65: 107 3.65 - 5.48: 14 5.48 - 7.31: 3 7.31 - 9.13: 1 Bond angle restraints: 7166 Sorted by residual: angle pdb=" N GLY X 345 " pdb=" CA GLY X 345 " pdb=" C GLY X 345 " ideal model delta sigma weight residual 111.21 114.15 -2.94 1.04e+00 9.25e-01 8.01e+00 angle pdb=" CA LEU X 475 " pdb=" CB LEU X 475 " pdb=" CG LEU X 475 " ideal model delta sigma weight residual 116.30 125.43 -9.13 3.50e+00 8.16e-02 6.81e+00 angle pdb=" CB MET X 672 " pdb=" CG MET X 672 " pdb=" SD MET X 672 " ideal model delta sigma weight residual 112.70 119.53 -6.83 3.00e+00 1.11e-01 5.19e+00 angle pdb=" CD ARG X 16 " pdb=" NE ARG X 16 " pdb=" CZ ARG X 16 " ideal model delta sigma weight residual 124.40 127.52 -3.12 1.40e+00 5.10e-01 4.97e+00 angle pdb=" N PRO X 556 " pdb=" CD PRO X 556 " pdb=" CG PRO X 556 " ideal model delta sigma weight residual 103.20 100.01 3.19 1.50e+00 4.44e-01 4.51e+00 ... (remaining 7161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 2786 17.85 - 35.69: 252 35.69 - 53.53: 95 53.53 - 71.38: 31 71.38 - 89.22: 17 Dihedral angle restraints: 3181 sinusoidal: 1277 harmonic: 1904 Sorted by residual: dihedral pdb=" CA ILE X 418 " pdb=" C ILE X 418 " pdb=" N SER X 419 " pdb=" CA SER X 419 " ideal model delta harmonic sigma weight residual -180.00 -162.43 -17.57 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CG ARG X 16 " pdb=" CD ARG X 16 " pdb=" NE ARG X 16 " pdb=" CZ ARG X 16 " ideal model delta sinusoidal sigma weight residual 90.00 41.19 48.81 2 1.50e+01 4.44e-03 1.21e+01 dihedral pdb=" CA LYS X 436 " pdb=" C LYS X 436 " pdb=" N TYR X 437 " pdb=" CA TYR X 437 " ideal model delta harmonic sigma weight residual 180.00 163.48 16.52 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 3178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 453 0.029 - 0.057: 225 0.057 - 0.086: 78 0.086 - 0.114: 42 0.114 - 0.143: 13 Chirality restraints: 811 Sorted by residual: chirality pdb=" CB THR X 407 " pdb=" CA THR X 407 " pdb=" OG1 THR X 407 " pdb=" CG2 THR X 407 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA ILE X 631 " pdb=" N ILE X 631 " pdb=" C ILE X 631 " pdb=" CB ILE X 631 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CG LEU X 531 " pdb=" CB LEU X 531 " pdb=" CD1 LEU X 531 " pdb=" CD2 LEU X 531 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 808 not shown) Planarity restraints: 923 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN X 555 " -0.027 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO X 556 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO X 556 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO X 556 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU X 339 " -0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO X 340 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO X 340 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO X 340 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG X 16 " 0.108 9.50e-02 1.11e+02 4.89e-02 1.87e+00 pdb=" NE ARG X 16 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG X 16 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG X 16 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG X 16 " 0.000 2.00e-02 2.50e+03 ... (remaining 920 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 722 2.76 - 3.30: 4743 3.30 - 3.83: 9669 3.83 - 4.37: 11275 4.37 - 4.90: 19023 Nonbonded interactions: 45432 Sorted by model distance: nonbonded pdb=" OE2 GLU X 331 " pdb=" OH TYR X 435 " model vdw 2.227 3.040 nonbonded pdb=" O PRO X 557 " pdb=" OG1 THR X 560 " model vdw 2.281 3.040 nonbonded pdb=" O LEU X 349 " pdb=" O HOH X 701 " model vdw 2.291 3.040 nonbonded pdb=" O LEU X 160 " pdb=" O HOH X 702 " model vdw 2.292 3.040 nonbonded pdb=" O ARG X 628 " pdb=" O HOH X 703 " model vdw 2.293 3.040 ... (remaining 45427 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.970 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 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 : 0.004 0.039 5281 Z= 0.242 Angle : 0.606 9.133 7166 Z= 0.320 Chirality : 0.043 0.143 811 Planarity : 0.005 0.049 923 Dihedral : 18.362 89.222 1947 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.15 % Allowed : 19.32 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.32), residues: 650 helix: 1.96 (0.47), residues: 114 sheet: 1.16 (0.32), residues: 255 loop : 0.80 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP X 205 HIS 0.005 0.001 HIS X 500 PHE 0.019 0.002 PHE X 639 TYR 0.021 0.002 TYR X 167 ARG 0.011 0.001 ARG X 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.540 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 103 average time/residue: 1.6175 time to fit residues: 172.4222 Evaluate side-chains 100 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 88 LYS Chi-restraints excluded: chain X residue 120 LEU Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 522 LEU Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 641 SER Chi-restraints excluded: chain X residue 659 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 0.0980 chunk 30 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 128 GLN X 175 GLN X 492 GLN X 600 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.0600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5281 Z= 0.219 Angle : 0.531 5.853 7166 Z= 0.278 Chirality : 0.043 0.145 811 Planarity : 0.004 0.033 923 Dihedral : 6.177 57.999 726 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 4.65 % Allowed : 17.35 % Favored : 78.00 % 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: 1.82 (0.32), residues: 650 helix: 2.24 (0.48), residues: 115 sheet: 1.26 (0.32), residues: 251 loop : 0.86 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP X 324 HIS 0.004 0.001 HIS X 22 PHE 0.020 0.002 PHE X 639 TYR 0.018 0.002 TYR X 167 ARG 0.005 0.000 ARG X 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.696 Fit side-chains REVERT: X 73 ASN cc_start: 0.8603 (m-40) cc_final: 0.8367 (m-40) REVERT: X 128 GLN cc_start: 0.7441 (mt0) cc_final: 0.7176 (tt0) REVERT: X 341 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7517 (tp40) outliers start: 26 outliers final: 15 residues processed: 106 average time/residue: 1.6431 time to fit residues: 180.6894 Evaluate side-chains 110 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 159 LEU Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 298 THR Chi-restraints excluded: chain X residue 341 GLN Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 442 LEU Chi-restraints excluded: chain X residue 445 LYS Chi-restraints excluded: chain X residue 508 GLN Chi-restraints excluded: chain X residue 522 LEU Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 611 GLN Chi-restraints excluded: chain X residue 648 MET Chi-restraints excluded: chain X residue 649 CYS Chi-restraints excluded: chain X residue 659 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 142 ASN X 175 GLN X 492 GLN X 538 ASN X 559 ASN X 600 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5281 Z= 0.338 Angle : 0.596 5.660 7166 Z= 0.313 Chirality : 0.046 0.153 811 Planarity : 0.005 0.034 923 Dihedral : 6.158 59.541 719 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 5.19 % Allowed : 17.17 % Favored : 77.64 % 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: 1.60 (0.32), residues: 650 helix: 2.17 (0.48), residues: 114 sheet: 1.12 (0.31), residues: 249 loop : 0.69 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP X 205 HIS 0.006 0.002 HIS X 22 PHE 0.026 0.002 PHE X 639 TYR 0.023 0.002 TYR X 167 ARG 0.004 0.000 ARG X 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.622 Fit side-chains REVERT: X 175 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.8030 (mp-120) REVERT: X 341 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7527 (tp40) REVERT: X 529 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8059 (tptp) outliers start: 29 outliers final: 14 residues processed: 111 average time/residue: 1.6227 time to fit residues: 186.2352 Evaluate side-chains 109 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 159 LEU Chi-restraints excluded: chain X residue 175 GLN Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 298 THR Chi-restraints excluded: chain X residue 341 GLN Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 442 LEU Chi-restraints excluded: chain X residue 445 LYS Chi-restraints excluded: chain X residue 522 LEU Chi-restraints excluded: chain X residue 529 LYS Chi-restraints excluded: chain X residue 611 GLN Chi-restraints excluded: chain X residue 648 MET Chi-restraints excluded: chain X residue 649 CYS Chi-restraints excluded: chain X residue 659 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 56 optimal weight: 0.0470 chunk 16 optimal weight: 6.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 128 GLN X 175 GLN X 492 GLN X 559 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5281 Z= 0.167 Angle : 0.495 5.314 7166 Z= 0.258 Chirality : 0.042 0.143 811 Planarity : 0.004 0.031 923 Dihedral : 5.259 52.235 717 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 4.11 % Allowed : 18.25 % Favored : 77.64 % 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 (0.33), residues: 650 helix: 2.42 (0.48), residues: 114 sheet: 1.08 (0.32), residues: 251 loop : 0.86 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 527 HIS 0.002 0.001 HIS X 22 PHE 0.017 0.001 PHE X 639 TYR 0.016 0.001 TYR X 167 ARG 0.007 0.000 ARG X 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.636 Fit side-chains REVERT: X 73 ASN cc_start: 0.8609 (m-40) cc_final: 0.8365 (m-40) REVERT: X 175 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7945 (mp-120) REVERT: X 341 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7494 (tp40) REVERT: X 529 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8081 (tptp) outliers start: 23 outliers final: 10 residues processed: 103 average time/residue: 1.7436 time to fit residues: 186.0281 Evaluate side-chains 107 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 159 LEU Chi-restraints excluded: chain X residue 175 GLN Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 298 THR Chi-restraints excluded: chain X residue 341 GLN Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 445 LYS Chi-restraints excluded: chain X residue 522 LEU Chi-restraints excluded: chain X residue 529 LYS Chi-restraints excluded: chain X residue 649 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 0.9980 chunk 35 optimal weight: 0.0050 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 0.0050 chunk 25 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 56 optimal weight: 0.0470 chunk 15 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 128 GLN X 142 ASN X 416 ASN X 492 GLN X 508 GLN X 559 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5281 Z= 0.119 Angle : 0.460 5.748 7166 Z= 0.239 Chirality : 0.041 0.158 811 Planarity : 0.003 0.033 923 Dihedral : 4.790 49.789 716 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.40 % Allowed : 19.50 % Favored : 77.10 % 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: 1.84 (0.33), residues: 650 helix: 2.45 (0.48), residues: 115 sheet: 1.16 (0.32), residues: 247 loop : 0.93 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 324 HIS 0.001 0.000 HIS X 210 PHE 0.015 0.001 PHE X 639 TYR 0.011 0.001 TYR X 167 ARG 0.008 0.000 ARG X 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.645 Fit side-chains REVERT: X 508 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7415 (tm130) outliers start: 19 outliers final: 10 residues processed: 103 average time/residue: 1.7708 time to fit residues: 188.8742 Evaluate side-chains 102 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain X residue 120 LEU Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 159 LEU Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 298 THR Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 456 MET Chi-restraints excluded: chain X residue 508 GLN Chi-restraints excluded: chain X residue 659 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 10.0000 chunk 12 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 175 GLN X 492 GLN X 559 ASN X 602 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5281 Z= 0.240 Angle : 0.526 5.492 7166 Z= 0.274 Chirality : 0.043 0.141 811 Planarity : 0.004 0.038 923 Dihedral : 5.108 53.033 714 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 4.29 % Allowed : 19.14 % Favored : 76.57 % 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: 1.81 (0.33), residues: 650 helix: 2.40 (0.48), residues: 114 sheet: 1.22 (0.32), residues: 243 loop : 0.83 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP X 205 HIS 0.004 0.001 HIS X 22 PHE 0.021 0.002 PHE X 639 TYR 0.020 0.002 TYR X 167 ARG 0.006 0.000 ARG X 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.546 Fit side-chains REVERT: X 341 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7446 (tt0) outliers start: 24 outliers final: 11 residues processed: 108 average time/residue: 1.6686 time to fit residues: 186.3306 Evaluate side-chains 110 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 159 LEU Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 298 THR Chi-restraints excluded: chain X residue 341 GLN Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 507 VAL Chi-restraints excluded: chain X residue 649 CYS Chi-restraints excluded: chain X residue 659 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 9.9990 chunk 35 optimal weight: 0.0060 chunk 45 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 62 optimal weight: 0.2980 chunk 39 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 overall best weight: 1.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 142 ASN X 492 GLN X 508 GLN X 559 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5281 Z= 0.180 Angle : 0.498 5.722 7166 Z= 0.259 Chirality : 0.042 0.135 811 Planarity : 0.004 0.036 923 Dihedral : 4.972 50.358 714 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.94 % Allowed : 19.68 % Favored : 76.39 % 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: 1.84 (0.33), residues: 650 helix: 2.47 (0.48), residues: 114 sheet: 1.15 (0.32), residues: 245 loop : 0.93 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP X 527 HIS 0.003 0.001 HIS X 22 PHE 0.019 0.001 PHE X 639 TYR 0.016 0.001 TYR X 167 ARG 0.008 0.000 ARG X 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.640 Fit side-chains outliers start: 22 outliers final: 14 residues processed: 110 average time/residue: 1.7828 time to fit residues: 203.0073 Evaluate side-chains 109 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 159 LEU Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 298 THR Chi-restraints excluded: chain X residue 362 SER Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 445 LYS Chi-restraints excluded: chain X residue 456 MET Chi-restraints excluded: chain X residue 507 VAL Chi-restraints excluded: chain X residue 607 SER Chi-restraints excluded: chain X residue 659 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 0.2980 chunk 39 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 175 GLN X 492 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5281 Z= 0.130 Angle : 0.458 5.527 7166 Z= 0.238 Chirality : 0.041 0.134 811 Planarity : 0.003 0.034 923 Dihedral : 4.707 47.850 714 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.40 % Allowed : 20.75 % Favored : 75.85 % 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 (0.33), residues: 650 helix: 2.51 (0.49), residues: 115 sheet: 1.20 (0.32), residues: 244 loop : 1.01 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 527 HIS 0.002 0.001 HIS X 517 PHE 0.015 0.001 PHE X 639 TYR 0.013 0.001 TYR X 167 ARG 0.009 0.000 ARG X 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.753 Fit side-chains REVERT: X 341 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7364 (tp40) outliers start: 19 outliers final: 13 residues processed: 104 average time/residue: 1.6764 time to fit residues: 180.4016 Evaluate side-chains 106 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain X residue 120 LEU Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 159 LEU Chi-restraints excluded: chain X residue 177 GLU Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 298 THR Chi-restraints excluded: chain X residue 341 GLN Chi-restraints excluded: chain X residue 362 SER Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 456 MET Chi-restraints excluded: chain X residue 507 VAL Chi-restraints excluded: chain X residue 659 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 0.0770 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 142 ASN X 175 GLN X 492 GLN X 508 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5281 Z= 0.213 Angle : 0.519 6.009 7166 Z= 0.270 Chirality : 0.042 0.139 811 Planarity : 0.004 0.040 923 Dihedral : 5.004 49.737 714 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.40 % Allowed : 20.93 % Favored : 75.67 % 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: 1.88 (0.33), residues: 650 helix: 2.46 (0.48), residues: 114 sheet: 1.19 (0.32), residues: 245 loop : 0.96 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP X 205 HIS 0.004 0.001 HIS X 22 PHE 0.020 0.002 PHE X 639 TYR 0.019 0.002 TYR X 167 ARG 0.007 0.000 ARG X 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.644 Fit side-chains REVERT: X 341 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7426 (tt0) outliers start: 19 outliers final: 10 residues processed: 109 average time/residue: 1.5838 time to fit residues: 179.1927 Evaluate side-chains 106 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain X residue 120 LEU Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 159 LEU Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 298 THR Chi-restraints excluded: chain X residue 341 GLN Chi-restraints excluded: chain X residue 362 SER Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 659 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 15 optimal weight: 0.4980 chunk 47 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 492 GLN X 602 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5281 Z= 0.193 Angle : 0.510 6.343 7166 Z= 0.265 Chirality : 0.042 0.138 811 Planarity : 0.004 0.038 923 Dihedral : 4.962 48.396 714 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.50 % Allowed : 21.47 % Favored : 76.03 % 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: 1.88 (0.33), residues: 650 helix: 2.48 (0.49), residues: 114 sheet: 1.19 (0.32), residues: 245 loop : 0.95 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 527 HIS 0.003 0.001 HIS X 22 PHE 0.020 0.001 PHE X 639 TYR 0.017 0.002 TYR X 167 ARG 0.008 0.000 ARG X 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.658 Fit side-chains REVERT: X 341 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7424 (tt0) outliers start: 14 outliers final: 10 residues processed: 107 average time/residue: 1.6140 time to fit residues: 178.6932 Evaluate side-chains 108 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain X residue 120 LEU Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 159 LEU Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 298 THR Chi-restraints excluded: chain X residue 341 GLN Chi-restraints excluded: chain X residue 362 SER Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 659 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 142 ASN X 175 GLN X 492 GLN X 508 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.123656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.101483 restraints weight = 4994.332| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.21 r_work: 0.2879 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5281 Z= 0.168 Angle : 0.496 6.461 7166 Z= 0.257 Chirality : 0.042 0.135 811 Planarity : 0.004 0.038 923 Dihedral : 4.857 47.073 714 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.22 % Allowed : 20.93 % Favored : 75.85 % 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 (0.33), residues: 650 helix: 2.53 (0.49), residues: 114 sheet: 1.21 (0.32), residues: 245 loop : 0.97 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 527 HIS 0.002 0.001 HIS X 22 PHE 0.019 0.001 PHE X 639 TYR 0.016 0.001 TYR X 167 ARG 0.008 0.000 ARG X 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3287.20 seconds wall clock time: 61 minutes 14.91 seconds (3674.91 seconds total)