Starting phenix.real_space_refine on Tue Feb 11 12:32:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u0j_41781/02_2025/8u0j_41781.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u0j_41781/02_2025/8u0j_41781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u0j_41781/02_2025/8u0j_41781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u0j_41781/02_2025/8u0j_41781.map" model { file = "/net/cci-nas-00/data/ceres_data/8u0j_41781/02_2025/8u0j_41781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u0j_41781/02_2025/8u0j_41781.cif" } resolution = 3.1 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= 0.061 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 P 48 5.49 5 Mg 1 5.21 5 S 10 5.16 5 C 3466 2.51 5 N 963 2.21 5 O 1169 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5657 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4669 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 540} Chain breaks: 1 Chain: "B" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 290 Classifications: {'DNA': 14} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 13} Chain: "D" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 471 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "F" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 226 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.41, per 1000 atoms: 0.78 Number of scatterers: 5657 At special positions: 0 Unit cell: (83.32, 81.6536, 102.484, 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) S 10 16.00 P 48 15.00 Mg 1 11.99 O 1169 8.00 N 963 7.00 C 3466 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: 1.56 Conformation dependent library (CDL) restraints added in 788.9 milliseconds 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1074 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 6 sheets defined 36.7% alpha, 13.2% beta 9 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 249 through 266 Processing helix chain 'A' and resid 285 through 301 Processing helix chain 'A' and resid 317 through 328 removed outlier: 3.618A pdb=" N THR A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 328 " --> pdb=" O HIS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.701A pdb=" N TYR A 355 " --> pdb=" O LYS A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 370 removed outlier: 3.834A pdb=" N VAL A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ARG A 367 " --> pdb=" O TYR A 363 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR A 370 " --> pdb=" O TYR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.529A pdb=" N TRP A 384 " --> pdb=" O GLU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 410 removed outlier: 4.174A pdb=" N VAL A 395 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 removed outlier: 4.015A pdb=" N ARG A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 473 removed outlier: 3.729A pdb=" N LEU A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 480 removed outlier: 4.310A pdb=" N ARG A 478 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N HIS A 479 " --> pdb=" O ASP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 528 removed outlier: 3.772A pdb=" N GLU A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 542 Processing helix chain 'A' and resid 547 through 558 Processing helix chain 'A' and resid 565 through 572 removed outlier: 3.535A pdb=" N GLU A 568 " --> pdb=" O PRO A 565 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR A 571 " --> pdb=" O GLU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 589 Processing helix chain 'A' and resid 649 through 657 removed outlier: 3.909A pdb=" N LEU A 655 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE A 656 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 657 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.808A pdb=" N LYS A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS A 675 " --> pdb=" O TYR A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 684 No H-bonds generated for 'chain 'A' and resid 682 through 684' Processing sheet with id=AA1, first strand: chain 'A' and resid 136 through 144 removed outlier: 5.757A pdb=" N TYR A 137 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE A 159 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU A 139 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 157 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 237 Processing sheet with id=AA4, first strand: chain 'A' and resid 334 through 336 removed outlier: 7.052A pdb=" N LEU A 305 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ALA A 336 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE A 307 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ASN A 345 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N CYS A 378 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU A 347 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 455 through 460 removed outlier: 7.228A pdb=" N LEU A 638 " --> pdb=" O THR A 504 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 506 " --> pdb=" O SER A 636 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N SER A 636 " --> pdb=" O ILE A 506 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 612 through 613 removed outlier: 3.917A pdb=" N PHE A 621 " --> pdb=" O PHE A 612 " (cutoff:3.500A) 154 hydrogen bonds defined for protein. 411 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 940 1.32 - 1.44: 1776 1.44 - 1.57: 3064 1.57 - 1.69: 93 1.69 - 1.81: 16 Bond restraints: 5889 Sorted by residual: bond pdb=" CB VAL A 680 " pdb=" CG1 VAL A 680 " ideal model delta sigma weight residual 1.521 1.418 0.103 3.30e-02 9.18e+02 9.67e+00 bond pdb=" C GLU A 416 " pdb=" N TYR A 417 " ideal model delta sigma weight residual 1.329 1.293 0.036 1.86e-02 2.89e+03 3.78e+00 bond pdb=" N SER A 436 " pdb=" CA SER A 436 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.19e+00 bond pdb=" CG PHE A 656 " pdb=" CD1 PHE A 656 " ideal model delta sigma weight residual 1.384 1.348 0.036 2.10e-02 2.27e+03 2.96e+00 bond pdb=" CB VAL A 251 " pdb=" CG1 VAL A 251 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.77e+00 ... (remaining 5884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 7783 2.00 - 3.99: 329 3.99 - 5.99: 43 5.99 - 7.98: 12 7.98 - 9.98: 2 Bond angle restraints: 8169 Sorted by residual: angle pdb=" C TYR A 363 " pdb=" N GLN A 364 " pdb=" CA GLN A 364 " ideal model delta sigma weight residual 121.54 131.52 -9.98 1.91e+00 2.74e-01 2.73e+01 angle pdb=" C PRO A 563 " pdb=" N LEU A 564 " pdb=" CA LEU A 564 " ideal model delta sigma weight residual 121.61 127.34 -5.73 1.39e+00 5.18e-01 1.70e+01 angle pdb=" C CYS A 378 " pdb=" N TYR A 379 " pdb=" CA TYR A 379 " ideal model delta sigma weight residual 121.48 129.48 -8.00 2.04e+00 2.40e-01 1.54e+01 angle pdb=" N SER A 608 " pdb=" CA SER A 608 " pdb=" C SER A 608 " ideal model delta sigma weight residual 114.09 108.35 5.74 1.55e+00 4.16e-01 1.37e+01 angle pdb=" C GLN A 430 " pdb=" N ARG A 431 " pdb=" CA ARG A 431 " ideal model delta sigma weight residual 120.94 127.94 -7.00 1.90e+00 2.77e-01 1.36e+01 ... (remaining 8164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 2770 17.94 - 35.88: 404 35.88 - 53.82: 189 53.82 - 71.76: 47 71.76 - 89.70: 9 Dihedral angle restraints: 3419 sinusoidal: 1749 harmonic: 1670 Sorted by residual: dihedral pdb=" CA SER A 437 " pdb=" C SER A 437 " pdb=" N GLU A 438 " pdb=" CA GLU A 438 " ideal model delta harmonic sigma weight residual -180.00 -125.52 -54.48 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA GLU A 435 " pdb=" C GLU A 435 " pdb=" N SER A 436 " pdb=" CA SER A 436 " ideal model delta harmonic sigma weight residual -180.00 -140.41 -39.59 0 5.00e+00 4.00e-02 6.27e+01 dihedral pdb=" CA TYR A 220 " pdb=" C TYR A 220 " pdb=" N ILE A 221 " pdb=" CA ILE A 221 " ideal model delta harmonic sigma weight residual 180.00 -158.53 -21.47 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 3416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 648 0.051 - 0.102: 186 0.102 - 0.153: 35 0.153 - 0.204: 8 0.204 - 0.255: 1 Chirality restraints: 878 Sorted by residual: chirality pdb=" CA PHE A 656 " pdb=" N PHE A 656 " pdb=" C PHE A 656 " pdb=" CB PHE A 656 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA GLN A 364 " pdb=" N GLN A 364 " pdb=" C GLN A 364 " pdb=" CB GLN A 364 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB VAL A 480 " pdb=" CA VAL A 480 " pdb=" CG1 VAL A 480 " pdb=" CG2 VAL A 480 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.04e-01 ... (remaining 875 not shown) Planarity restraints: 889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 364 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C GLN A 364 " 0.058 2.00e-02 2.50e+03 pdb=" O GLN A 364 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL A 365 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 428 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.12e+00 pdb=" N PRO A 429 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 429 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 429 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 363 " 0.015 2.00e-02 2.50e+03 1.39e-02 3.84e+00 pdb=" CG TYR A 363 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 363 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 363 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 363 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 363 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 363 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 363 " -0.000 2.00e-02 2.50e+03 ... (remaining 886 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 313 2.72 - 3.26: 5253 3.26 - 3.81: 9454 3.81 - 4.35: 11941 4.35 - 4.90: 19173 Nonbonded interactions: 46134 Sorted by model distance: nonbonded pdb=" OP1 DT B 3 " pdb="MG MG B 101 " model vdw 2.170 2.170 nonbonded pdb=" OH TYR A 620 " pdb=" O VAL A 668 " model vdw 2.204 3.040 nonbonded pdb=" OG SER A 576 " pdb=" OP1 DA D 23 " model vdw 2.250 3.040 nonbonded pdb=" NH1 ARG A 202 " pdb=" O GLY A 218 " model vdw 2.256 3.120 nonbonded pdb=" O2 DT D 20 " pdb=" N2 DG F 9 " model vdw 2.300 3.120 ... (remaining 46129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 3.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 19.290 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.103 5889 Z= 0.472 Angle : 0.915 9.980 8169 Z= 0.526 Chirality : 0.050 0.255 878 Planarity : 0.006 0.057 889 Dihedral : 20.282 89.698 2345 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -1.07 (0.34), residues: 565 helix: 0.11 (0.40), residues: 154 sheet: -0.19 (0.53), residues: 90 loop : -1.30 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 444 HIS 0.006 0.002 HIS A 660 PHE 0.025 0.003 PHE A 685 TYR 0.034 0.003 TYR A 363 ARG 0.017 0.001 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.536 Fit side-chains REVERT: A 302 GLU cc_start: 0.7306 (tp30) cc_final: 0.6769 (tm-30) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2240 time to fit residues: 24.0885 Evaluate side-chains 72 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.229905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.183071 restraints weight = 6448.613| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 3.22 r_work: 0.3956 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 5889 Z= 0.262 Angle : 0.644 7.507 8169 Z= 0.355 Chirality : 0.042 0.153 878 Planarity : 0.006 0.044 889 Dihedral : 23.030 74.002 1166 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.98 % Allowed : 8.43 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.71 (0.35), residues: 565 helix: 0.75 (0.41), residues: 157 sheet: -0.07 (0.53), residues: 91 loop : -1.25 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 585 HIS 0.004 0.001 HIS A 281 PHE 0.025 0.002 PHE A 611 TYR 0.015 0.002 TYR A 293 ARG 0.004 0.000 ARG A 615 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.521 Fit side-chains REVERT: A 19 GLU cc_start: 0.5937 (tp30) cc_final: 0.5721 (tp30) REVERT: A 302 GLU cc_start: 0.7851 (tp30) cc_final: 0.7174 (tm-30) REVERT: A 440 ARG cc_start: 0.6724 (mmm160) cc_final: 0.5865 (mmm160) outliers start: 5 outliers final: 3 residues processed: 84 average time/residue: 0.2037 time to fit residues: 22.1507 Evaluate side-chains 80 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 597 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 43 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4532 r_free = 0.4532 target = 0.228215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.181124 restraints weight = 6480.029| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 3.25 r_work: 0.3931 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 5889 Z= 0.297 Angle : 0.639 6.850 8169 Z= 0.350 Chirality : 0.042 0.156 878 Planarity : 0.005 0.043 889 Dihedral : 23.083 77.411 1166 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 1.37 % Allowed : 12.75 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.59 (0.36), residues: 565 helix: 0.97 (0.41), residues: 157 sheet: 0.01 (0.52), residues: 94 loop : -1.27 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 456 HIS 0.006 0.001 HIS A 281 PHE 0.014 0.002 PHE A 621 TYR 0.015 0.002 TYR A 671 ARG 0.002 0.000 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.586 Fit side-chains REVERT: A 302 GLU cc_start: 0.7862 (tp30) cc_final: 0.7259 (tm-30) REVERT: A 341 ARG cc_start: 0.7349 (mtm110) cc_final: 0.6616 (mtp180) REVERT: A 440 ARG cc_start: 0.6748 (mmm160) cc_final: 0.5606 (mmm160) outliers start: 7 outliers final: 4 residues processed: 85 average time/residue: 0.1975 time to fit residues: 21.7098 Evaluate side-chains 78 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 597 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 44 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN A 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.226839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.181817 restraints weight = 6501.490| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 3.10 r_work: 0.3953 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 5889 Z= 0.274 Angle : 0.615 6.419 8169 Z= 0.336 Chirality : 0.041 0.156 878 Planarity : 0.005 0.044 889 Dihedral : 22.985 71.324 1166 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.96 % Allowed : 13.33 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.44 (0.36), residues: 565 helix: 1.18 (0.41), residues: 156 sheet: -0.02 (0.53), residues: 92 loop : -1.16 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 444 HIS 0.004 0.001 HIS A 281 PHE 0.027 0.002 PHE A 611 TYR 0.013 0.002 TYR A 671 ARG 0.003 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.557 Fit side-chains REVERT: A 302 GLU cc_start: 0.7838 (tp30) cc_final: 0.7268 (tm-30) REVERT: A 341 ARG cc_start: 0.7312 (mtm110) cc_final: 0.6614 (mtp180) REVERT: A 440 ARG cc_start: 0.6710 (mmm160) cc_final: 0.5909 (mmm160) REVERT: A 611 PHE cc_start: 0.7429 (t80) cc_final: 0.7049 (t80) REVERT: A 633 GLU cc_start: 0.8271 (pm20) cc_final: 0.7389 (pt0) outliers start: 10 outliers final: 6 residues processed: 85 average time/residue: 0.2182 time to fit residues: 23.5635 Evaluate side-chains 81 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 53 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 44 optimal weight: 0.0170 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 24 optimal weight: 0.5980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 = 0.4566 r_free = 0.4566 target = 0.232041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.185750 restraints weight = 6484.322| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 3.22 r_work: 0.3981 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5889 Z= 0.207 Angle : 0.572 6.218 8169 Z= 0.315 Chirality : 0.039 0.151 878 Planarity : 0.005 0.045 889 Dihedral : 22.811 69.048 1166 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.18 % Allowed : 15.29 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.22 (0.36), residues: 565 helix: 1.44 (0.41), residues: 157 sheet: 0.06 (0.53), residues: 92 loop : -1.07 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 444 HIS 0.002 0.001 HIS A 643 PHE 0.021 0.002 PHE A 611 TYR 0.011 0.001 TYR A 491 ARG 0.002 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.515 Fit side-chains REVERT: A 302 GLU cc_start: 0.7798 (tp30) cc_final: 0.7258 (tm-30) REVERT: A 341 ARG cc_start: 0.7332 (mtm110) cc_final: 0.6615 (mtp180) REVERT: A 371 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7449 (mm-40) REVERT: A 440 ARG cc_start: 0.6541 (mmm160) cc_final: 0.5633 (mmm160) REVERT: A 486 ARG cc_start: 0.7724 (mtt180) cc_final: 0.7481 (mtt180) REVERT: A 578 ASP cc_start: 0.8295 (t0) cc_final: 0.8053 (t0) REVERT: A 619 MET cc_start: 0.5720 (mtm) cc_final: 0.5410 (mtm) REVERT: A 633 GLU cc_start: 0.8294 (pm20) cc_final: 0.7298 (pt0) outliers start: 6 outliers final: 6 residues processed: 84 average time/residue: 0.2094 time to fit residues: 22.3678 Evaluate side-chains 79 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 49 optimal weight: 0.0770 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.4565 r_free = 0.4565 target = 0.232374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.188468 restraints weight = 6377.969| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 3.03 r_work: 0.4005 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5889 Z= 0.202 Angle : 0.562 5.965 8169 Z= 0.308 Chirality : 0.039 0.149 878 Planarity : 0.005 0.046 889 Dihedral : 22.786 70.089 1166 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.57 % Allowed : 15.88 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.04 (0.37), residues: 565 helix: 1.62 (0.42), residues: 157 sheet: 0.09 (0.54), residues: 92 loop : -0.94 (0.38), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 444 HIS 0.002 0.000 HIS A 643 PHE 0.014 0.002 PHE A 685 TYR 0.012 0.001 TYR A 671 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.513 Fit side-chains REVERT: A 302 GLU cc_start: 0.7814 (tp30) cc_final: 0.7257 (tm-30) REVERT: A 341 ARG cc_start: 0.7304 (mtm110) cc_final: 0.6607 (mtp180) REVERT: A 371 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7410 (mm-40) REVERT: A 417 TYR cc_start: 0.7691 (m-80) cc_final: 0.7341 (m-80) REVERT: A 440 ARG cc_start: 0.6540 (mmm160) cc_final: 0.5601 (mmm160) REVERT: A 486 ARG cc_start: 0.7750 (mtt180) cc_final: 0.7387 (mtt180) REVERT: A 619 MET cc_start: 0.5634 (mtm) cc_final: 0.5341 (mtm) REVERT: A 633 GLU cc_start: 0.8282 (pm20) cc_final: 0.7671 (pm20) outliers start: 8 outliers final: 7 residues processed: 84 average time/residue: 0.2108 time to fit residues: 22.6131 Evaluate side-chains 78 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4557 r_free = 0.4557 target = 0.231012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.184338 restraints weight = 6515.102| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 3.22 r_work: 0.3967 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5889 Z= 0.249 Angle : 0.591 5.859 8169 Z= 0.322 Chirality : 0.040 0.152 878 Planarity : 0.005 0.047 889 Dihedral : 22.907 73.312 1166 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 1.37 % Allowed : 16.67 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.12 (0.37), residues: 565 helix: 1.59 (0.41), residues: 156 sheet: 0.04 (0.53), residues: 92 loop : -1.00 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 444 HIS 0.003 0.001 HIS A 643 PHE 0.014 0.002 PHE A 685 TYR 0.013 0.002 TYR A 671 ARG 0.001 0.000 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.569 Fit side-chains REVERT: A 302 GLU cc_start: 0.7884 (tp30) cc_final: 0.7229 (tm-30) REVERT: A 341 ARG cc_start: 0.7309 (mtm110) cc_final: 0.6565 (mtp180) REVERT: A 417 TYR cc_start: 0.7732 (m-80) cc_final: 0.7348 (m-80) REVERT: A 440 ARG cc_start: 0.6527 (mmm160) cc_final: 0.5467 (mmm160) REVERT: A 619 MET cc_start: 0.5742 (mtm) cc_final: 0.5406 (mtm) REVERT: A 633 GLU cc_start: 0.8258 (pm20) cc_final: 0.7040 (pt0) outliers start: 7 outliers final: 7 residues processed: 77 average time/residue: 0.1942 time to fit residues: 19.1808 Evaluate side-chains 72 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 9 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.229775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.182953 restraints weight = 6376.312| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 3.18 r_work: 0.3953 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5889 Z= 0.271 Angle : 0.605 6.534 8169 Z= 0.328 Chirality : 0.041 0.151 878 Planarity : 0.005 0.046 889 Dihedral : 22.932 73.835 1166 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 1.76 % Allowed : 16.08 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.18 (0.36), residues: 565 helix: 1.55 (0.42), residues: 156 sheet: 0.01 (0.52), residues: 92 loop : -1.04 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 444 HIS 0.003 0.001 HIS A 643 PHE 0.025 0.002 PHE A 621 TYR 0.013 0.002 TYR A 671 ARG 0.002 0.000 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.507 Fit side-chains REVERT: A 302 GLU cc_start: 0.7862 (tp30) cc_final: 0.7181 (tm-30) REVERT: A 341 ARG cc_start: 0.7308 (mtm110) cc_final: 0.6581 (mtp85) REVERT: A 364 GLN cc_start: 0.6230 (OUTLIER) cc_final: 0.5853 (pt0) REVERT: A 417 TYR cc_start: 0.7763 (m-80) cc_final: 0.7358 (m-80) REVERT: A 435 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7083 (pm20) REVERT: A 440 ARG cc_start: 0.6461 (mmm160) cc_final: 0.5308 (mmm160) REVERT: A 619 MET cc_start: 0.5802 (mtm) cc_final: 0.5462 (mtm) REVERT: A 633 GLU cc_start: 0.8332 (pm20) cc_final: 0.7384 (pm20) outliers start: 9 outliers final: 8 residues processed: 77 average time/residue: 0.2064 time to fit residues: 20.5994 Evaluate side-chains 76 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 364 GLN Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 chunk 12 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 0.0470 chunk 4 optimal weight: 2.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 GLN A 482 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.234793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.188364 restraints weight = 6438.298| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 3.21 r_work: 0.4005 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5889 Z= 0.192 Angle : 0.562 5.774 8169 Z= 0.307 Chirality : 0.039 0.149 878 Planarity : 0.005 0.046 889 Dihedral : 22.751 69.619 1166 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.76 % Allowed : 16.47 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.08 (0.37), residues: 565 helix: 1.84 (0.42), residues: 156 sheet: 0.24 (0.53), residues: 92 loop : -0.95 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 492 HIS 0.002 0.000 HIS A 281 PHE 0.020 0.002 PHE A 621 TYR 0.011 0.001 TYR A 491 ARG 0.001 0.000 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.573 Fit side-chains REVERT: A 302 GLU cc_start: 0.7820 (tp30) cc_final: 0.7145 (tm-30) REVERT: A 341 ARG cc_start: 0.7294 (mtm110) cc_final: 0.6549 (mtp180) REVERT: A 364 GLN cc_start: 0.6120 (OUTLIER) cc_final: 0.5734 (pt0) REVERT: A 435 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7286 (pm20) REVERT: A 440 ARG cc_start: 0.6361 (mmm160) cc_final: 0.5208 (mmm160) REVERT: A 619 MET cc_start: 0.5622 (mtm) cc_final: 0.5340 (mtm) REVERT: A 633 GLU cc_start: 0.8297 (pm20) cc_final: 0.7400 (pm20) outliers start: 9 outliers final: 6 residues processed: 78 average time/residue: 0.2045 time to fit residues: 20.8745 Evaluate side-chains 78 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 364 GLN Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 0.2980 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.234082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.187492 restraints weight = 6527.497| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 3.23 r_work: 0.3995 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5889 Z= 0.209 Angle : 0.573 6.373 8169 Z= 0.311 Chirality : 0.039 0.149 878 Planarity : 0.005 0.045 889 Dihedral : 22.774 72.325 1166 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.37 % Allowed : 16.67 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.07 (0.37), residues: 565 helix: 1.82 (0.42), residues: 156 sheet: 0.19 (0.52), residues: 93 loop : -0.94 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 444 HIS 0.002 0.001 HIS A 643 PHE 0.022 0.002 PHE A 621 TYR 0.012 0.001 TYR A 671 ARG 0.003 0.000 ARG A 367 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.528 Fit side-chains REVERT: A 302 GLU cc_start: 0.7807 (tp30) cc_final: 0.7292 (tm-30) REVERT: A 341 ARG cc_start: 0.7294 (mtm110) cc_final: 0.6557 (mtp180) REVERT: A 364 GLN cc_start: 0.5922 (OUTLIER) cc_final: 0.5505 (pt0) REVERT: A 440 ARG cc_start: 0.6425 (mmm160) cc_final: 0.5313 (mmm160) REVERT: A 486 ARG cc_start: 0.7765 (mtt180) cc_final: 0.7256 (mtt180) REVERT: A 619 MET cc_start: 0.5634 (mtm) cc_final: 0.5330 (mtm) REVERT: A 633 GLU cc_start: 0.8309 (pm20) cc_final: 0.7599 (pm20) outliers start: 7 outliers final: 6 residues processed: 79 average time/residue: 0.1972 time to fit residues: 20.0293 Evaluate side-chains 79 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 364 GLN Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 0.0970 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 25 optimal weight: 0.0970 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 29 optimal weight: 0.0970 overall best weight: 0.1974 ------------------------------------------------------------------------------- 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 = 0.4625 r_free = 0.4625 target = 0.238857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.193262 restraints weight = 6531.286| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 3.22 r_work: 0.4055 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5889 Z= 0.167 Angle : 0.553 5.659 8169 Z= 0.301 Chirality : 0.038 0.145 878 Planarity : 0.005 0.046 889 Dihedral : 22.645 70.018 1166 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.98 % Allowed : 17.65 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.25 (0.37), residues: 565 helix: 2.05 (0.42), residues: 157 sheet: 0.33 (0.52), residues: 93 loop : -0.89 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 492 HIS 0.005 0.001 HIS A 292 PHE 0.021 0.001 PHE A 621 TYR 0.011 0.001 TYR A 491 ARG 0.001 0.000 ARG A 367 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2890.24 seconds wall clock time: 52 minutes 7.56 seconds (3127.56 seconds total)