Starting phenix.real_space_refine on Tue Feb 11 11:51:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wua_37852/02_2025/8wua_37852.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wua_37852/02_2025/8wua_37852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wua_37852/02_2025/8wua_37852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wua_37852/02_2025/8wua_37852.map" model { file = "/net/cci-nas-00/data/ceres_data/8wua_37852/02_2025/8wua_37852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wua_37852/02_2025/8wua_37852.cif" } resolution = 3.6 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= 0.003 sd= 0.056 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 38 5.16 5 C 3622 2.51 5 N 888 2.21 5 O 946 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5494 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5494 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 26, 'TRANS': 648} Chain breaks: 1 Time building chain proxies: 3.76, per 1000 atoms: 0.68 Number of scatterers: 5494 At special positions: 0 Unit cell: (91.1257, 96.6152, 92.2236, 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 38 16.00 O 946 8.00 N 888 7.00 C 3622 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 32 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 315 " distance=2.03 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: 1.35 Conformation dependent library (CDL) restraints added in 666.7 milliseconds 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1292 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 2 sheets defined 65.2% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 13 through 18 removed outlier: 4.130A pdb=" N ARG A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 21 No H-bonds generated for 'chain 'A' and resid 19 through 21' Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 49 through 75 removed outlier: 3.712A pdb=" N VAL A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 removed outlier: 4.001A pdb=" N ILE A 120 " --> pdb=" O TRP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 134 through 158 removed outlier: 3.791A pdb=" N HIS A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 167 removed outlier: 3.822A pdb=" N VAL A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 182 removed outlier: 3.749A pdb=" N THR A 181 " --> pdb=" O PHE A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 219 removed outlier: 3.793A pdb=" N HIS A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 205 " --> pdb=" O VAL A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 252 Processing helix chain 'A' and resid 266 through 294 Processing helix chain 'A' and resid 304 through 308 removed outlier: 4.116A pdb=" N PHE A 307 " --> pdb=" O CYS A 304 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS A 308 " --> pdb=" O GLY A 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 308' Processing helix chain 'A' and resid 320 through 341 removed outlier: 3.651A pdb=" N ARG A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 345 removed outlier: 3.753A pdb=" N GLN A 345 " --> pdb=" O VAL A 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 342 through 345' Processing helix chain 'A' and resid 357 through 365 Processing helix chain 'A' and resid 415 through 445 removed outlier: 3.915A pdb=" N TRP A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR A 428 " --> pdb=" O GLY A 424 " (cutoff:3.500A) Proline residue: A 439 - end of helix Processing helix chain 'A' and resid 466 through 491 Proline residue: A 480 - end of helix Processing helix chain 'A' and resid 494 through 515 removed outlier: 4.153A pdb=" N ASN A 499 " --> pdb=" O LYS A 495 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLN A 500 " --> pdb=" O SER A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 534 Processing helix chain 'A' and resid 550 through 553 Processing helix chain 'A' and resid 554 through 565 Processing helix chain 'A' and resid 565 through 574 Processing helix chain 'A' and resid 574 through 587 Processing helix chain 'A' and resid 594 through 599 removed outlier: 3.767A pdb=" N LYS A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN A 599 " --> pdb=" O ARG A 595 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 594 through 599' Processing helix chain 'A' and resid 606 through 624 Processing helix chain 'A' and resid 630 through 650 removed outlier: 3.984A pdb=" N PHE A 634 " --> pdb=" O ILE A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 673 removed outlier: 3.598A pdb=" N ALA A 673 " --> pdb=" O ASN A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 690 Processing helix chain 'A' and resid 694 through 710 removed outlier: 3.588A pdb=" N LEU A 698 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 717 removed outlier: 4.042A pdb=" N PHE A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 262 removed outlier: 3.814A pdb=" N ILE A 232 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL A 352 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR A 396 " --> pdb=" O THR A 233 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 299 301 hydrogen bonds defined for protein. 891 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: 1.45 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1673 1.35 - 1.46: 1428 1.46 - 1.58: 2487 1.58 - 1.70: 2 1.70 - 1.81: 53 Bond restraints: 5643 Sorted by residual: bond pdb=" CB PRO A 439 " pdb=" CG PRO A 439 " ideal model delta sigma weight residual 1.492 1.654 -0.162 5.00e-02 4.00e+02 1.05e+01 bond pdb=" CB PRO A 576 " pdb=" CG PRO A 576 " ideal model delta sigma weight residual 1.492 1.602 -0.110 5.00e-02 4.00e+02 4.88e+00 bond pdb=" N PRO A 439 " pdb=" CD PRO A 439 " ideal model delta sigma weight residual 1.473 1.498 -0.025 1.40e-02 5.10e+03 3.15e+00 bond pdb=" N PRO A 439 " pdb=" CA PRO A 439 " ideal model delta sigma weight residual 1.470 1.449 0.021 1.34e-02 5.57e+03 2.55e+00 bond pdb=" CG PRO A 439 " pdb=" CD PRO A 439 " ideal model delta sigma weight residual 1.503 1.450 0.053 3.40e-02 8.65e+02 2.46e+00 ... (remaining 5638 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 7602 3.23 - 6.45: 44 6.45 - 9.68: 12 9.68 - 12.91: 5 12.91 - 16.14: 2 Bond angle restraints: 7665 Sorted by residual: angle pdb=" CA PRO A 439 " pdb=" N PRO A 439 " pdb=" CD PRO A 439 " ideal model delta sigma weight residual 112.00 95.86 16.14 1.40e+00 5.10e-01 1.33e+02 angle pdb=" CA PRO A 576 " pdb=" N PRO A 576 " pdb=" CD PRO A 576 " ideal model delta sigma weight residual 112.00 101.38 10.62 1.40e+00 5.10e-01 5.75e+01 angle pdb=" N PRO A 439 " pdb=" CD PRO A 439 " pdb=" CG PRO A 439 " ideal model delta sigma weight residual 103.20 95.89 7.31 1.50e+00 4.44e-01 2.38e+01 angle pdb=" CA MET A 327 " pdb=" CB MET A 327 " pdb=" CG MET A 327 " ideal model delta sigma weight residual 114.10 122.70 -8.60 2.00e+00 2.50e-01 1.85e+01 angle pdb=" CA LEU A 471 " pdb=" CB LEU A 471 " pdb=" CG LEU A 471 " ideal model delta sigma weight residual 116.30 130.57 -14.27 3.50e+00 8.16e-02 1.66e+01 ... (remaining 7660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 2943 18.00 - 36.00: 273 36.00 - 54.00: 85 54.00 - 72.00: 5 72.00 - 90.00: 7 Dihedral angle restraints: 3313 sinusoidal: 1321 harmonic: 1992 Sorted by residual: dihedral pdb=" CB CYS A 308 " pdb=" SG CYS A 308 " pdb=" SG CYS A 315 " pdb=" CB CYS A 315 " ideal model delta sinusoidal sigma weight residual -86.00 -20.15 -65.85 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CB CYS A 32 " pdb=" SG CYS A 32 " pdb=" SG CYS A 546 " pdb=" CB CYS A 546 " ideal model delta sinusoidal sigma weight residual 93.00 36.01 56.99 1 1.00e+01 1.00e-02 4.37e+01 dihedral pdb=" CA ASP A 366 " pdb=" C ASP A 366 " pdb=" N PHE A 367 " pdb=" CA PHE A 367 " ideal model delta harmonic sigma weight residual 180.00 -161.76 -18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 3310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 752 0.057 - 0.115: 115 0.115 - 0.172: 5 0.172 - 0.229: 1 0.229 - 0.286: 2 Chirality restraints: 875 Sorted by residual: chirality pdb=" CA PRO A 439 " pdb=" N PRO A 439 " pdb=" C PRO A 439 " pdb=" CB PRO A 439 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA PRO A 576 " pdb=" N PRO A 576 " pdb=" C PRO A 576 " pdb=" CB PRO A 576 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA MET A 327 " pdb=" N MET A 327 " pdb=" C MET A 327 " pdb=" CB MET A 327 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.42e-01 ... (remaining 872 not shown) Planarity restraints: 941 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 438 " -0.084 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO A 439 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO A 439 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 439 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 575 " -0.070 5.00e-02 4.00e+02 9.88e-02 1.56e+01 pdb=" N PRO A 576 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 576 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 576 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 529 " -0.017 2.00e-02 2.50e+03 1.94e-02 6.59e+00 pdb=" CG PHE A 529 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 529 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 529 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 529 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 529 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 529 " -0.000 2.00e-02 2.50e+03 ... (remaining 938 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 65 2.66 - 3.22: 5218 3.22 - 3.78: 8354 3.78 - 4.34: 10099 4.34 - 4.90: 16539 Nonbonded interactions: 40275 Sorted by model distance: nonbonded pdb=" O TRP A 531 " pdb=" OG1 THR A 536 " model vdw 2.105 3.040 nonbonded pdb=" O ALA A 694 " pdb=" OG1 THR A 697 " model vdw 2.321 3.040 nonbonded pdb=" NE1 TRP A 418 " pdb=" OE2 GLU A 490 " model vdw 2.378 3.120 nonbonded pdb=" NZ LYS A 371 " pdb=" O VAL A 397 " model vdw 2.381 3.120 nonbonded pdb=" OE1 GLN A 465 " pdb=" ND2 ASN A 558 " model vdw 2.383 3.120 ... (remaining 40270 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.510 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5848 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 0.162 5643 Z= 0.208 Angle : 0.750 16.137 7665 Z= 0.376 Chirality : 0.041 0.286 875 Planarity : 0.006 0.114 941 Dihedral : 15.346 89.998 2015 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.49 % Allowed : 23.03 % Favored : 76.48 % 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: 0.31 (0.33), residues: 671 helix: 1.41 (0.27), residues: 399 sheet: 0.65 (1.91), residues: 10 loop : -1.80 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 131 HIS 0.003 0.001 HIS A 648 PHE 0.045 0.001 PHE A 529 TYR 0.014 0.001 TYR A 203 ARG 0.003 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 MET cc_start: 0.6903 (mpp) cc_final: 0.6329 (pmm) REVERT: A 413 ILE cc_start: 0.6200 (mt) cc_final: 0.5987 (pt) REVERT: A 513 MET cc_start: 0.8271 (tmm) cc_final: 0.7846 (tmm) outliers start: 3 outliers final: 2 residues processed: 78 average time/residue: 0.1416 time to fit residues: 15.5854 Evaluate side-chains 74 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 220 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 0.0050 chunk 27 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.172052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.145806 restraints weight = 14605.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.149693 restraints weight = 7849.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.152157 restraints weight = 5159.987| |-----------------------------------------------------------------------------| r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5643 Z= 0.173 Angle : 0.600 10.934 7665 Z= 0.287 Chirality : 0.040 0.140 875 Planarity : 0.004 0.048 941 Dihedral : 4.366 46.647 733 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.45 % Allowed : 20.07 % Favored : 76.48 % 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: 0.23 (0.34), residues: 671 helix: 1.36 (0.27), residues: 407 sheet: 0.24 (1.43), residues: 17 loop : -2.00 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 395 HIS 0.006 0.001 HIS A 213 PHE 0.033 0.001 PHE A 529 TYR 0.015 0.001 TYR A 323 ARG 0.004 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.652 Fit side-chains REVERT: A 74 ARG cc_start: 0.4838 (ptm160) cc_final: 0.4153 (tpt170) REVERT: A 327 MET cc_start: 0.6945 (mpp) cc_final: 0.6590 (ptp) REVERT: A 413 ILE cc_start: 0.7160 (OUTLIER) cc_final: 0.6834 (pt) REVERT: A 437 THR cc_start: 0.6395 (m) cc_final: 0.6162 (t) REVERT: A 614 MET cc_start: 0.7868 (ttm) cc_final: 0.7644 (ttm) REVERT: A 627 THR cc_start: 0.7908 (m) cc_final: 0.7377 (p) outliers start: 21 outliers final: 11 residues processed: 97 average time/residue: 0.1252 time to fit residues: 17.5020 Evaluate side-chains 93 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 14 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 51 optimal weight: 0.0370 chunk 26 optimal weight: 0.9990 overall best weight: 0.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.157338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.128220 restraints weight = 14543.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.131976 restraints weight = 7709.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.134367 restraints weight = 5105.056| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5643 Z= 0.189 Angle : 0.627 11.448 7665 Z= 0.298 Chirality : 0.041 0.152 875 Planarity : 0.004 0.035 941 Dihedral : 4.007 35.401 731 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.28 % Allowed : 21.22 % Favored : 74.51 % 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: 0.28 (0.34), residues: 671 helix: 1.42 (0.27), residues: 406 sheet: -0.23 (1.40), residues: 17 loop : -1.95 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 395 HIS 0.005 0.001 HIS A 213 PHE 0.035 0.001 PHE A 529 TYR 0.015 0.001 TYR A 362 ARG 0.003 0.001 ARG A 543 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.4576 (ptm160) cc_final: 0.4038 (tpt170) REVERT: A 156 LEU cc_start: 0.8906 (tp) cc_final: 0.8688 (pp) REVERT: A 265 ASN cc_start: 0.8829 (t0) cc_final: 0.8617 (t0) REVERT: A 270 ILE cc_start: 0.7743 (mm) cc_final: 0.7430 (mm) REVERT: A 327 MET cc_start: 0.7188 (mpp) cc_final: 0.6912 (ptp) REVERT: A 413 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7295 (pt) REVERT: A 449 PHE cc_start: 0.7826 (m-80) cc_final: 0.7379 (m-80) REVERT: A 525 LEU cc_start: 0.8121 (mt) cc_final: 0.7891 (mt) REVERT: A 532 LEU cc_start: 0.5695 (mm) cc_final: 0.5454 (mm) REVERT: A 544 LEU cc_start: 0.8072 (pt) cc_final: 0.7584 (pp) REVERT: A 545 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8263 (pp20) REVERT: A 683 TYR cc_start: 0.7737 (t80) cc_final: 0.7268 (t80) outliers start: 26 outliers final: 12 residues processed: 118 average time/residue: 0.1289 time to fit residues: 21.3458 Evaluate side-chains 107 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 35 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 27 optimal weight: 8.9990 chunk 47 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 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 604 GLN A 664 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.152151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.122514 restraints weight = 14793.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.126184 restraints weight = 7638.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.128492 restraints weight = 5037.518| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5643 Z= 0.175 Angle : 0.592 10.451 7665 Z= 0.286 Chirality : 0.040 0.127 875 Planarity : 0.003 0.037 941 Dihedral : 3.636 16.792 729 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.77 % Allowed : 21.22 % Favored : 74.01 % 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: 0.36 (0.34), residues: 671 helix: 1.50 (0.27), residues: 408 sheet: -0.48 (1.33), residues: 17 loop : -1.97 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 473 HIS 0.006 0.001 HIS A 213 PHE 0.041 0.001 PHE A 529 TYR 0.009 0.001 TYR A 624 ARG 0.002 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.4545 (ptm160) cc_final: 0.3925 (tpt170) REVERT: A 270 ILE cc_start: 0.8252 (mm) cc_final: 0.7927 (mm) REVERT: A 413 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7427 (pt) REVERT: A 544 LEU cc_start: 0.8402 (pt) cc_final: 0.7937 (pp) outliers start: 29 outliers final: 19 residues processed: 105 average time/residue: 0.1273 time to fit residues: 19.0095 Evaluate side-chains 105 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 41 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 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 = 0.4107 r_free = 0.4107 target = 0.140333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.109289 restraints weight = 13759.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.112951 restraints weight = 7115.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.115318 restraints weight = 4669.214| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.6053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5643 Z= 0.207 Angle : 0.642 10.332 7665 Z= 0.310 Chirality : 0.042 0.191 875 Planarity : 0.003 0.035 941 Dihedral : 3.839 18.629 729 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 5.26 % Allowed : 21.55 % Favored : 73.19 % 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: 0.36 (0.34), residues: 671 helix: 1.50 (0.27), residues: 406 sheet: -0.41 (1.29), residues: 17 loop : -1.95 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 395 HIS 0.005 0.001 HIS A 213 PHE 0.043 0.001 PHE A 529 TYR 0.009 0.001 TYR A 624 ARG 0.004 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 270 ILE cc_start: 0.8349 (mm) cc_final: 0.8032 (mm) REVERT: A 427 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7028 (t80) outliers start: 32 outliers final: 26 residues processed: 108 average time/residue: 0.1267 time to fit residues: 19.8273 Evaluate side-chains 110 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 4 optimal weight: 0.9980 chunk 42 optimal weight: 0.1980 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 30 optimal weight: 0.0010 chunk 57 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** 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 = 0.4116 r_free = 0.4116 target = 0.141057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.110553 restraints weight = 13568.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.114303 restraints weight = 6841.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.116730 restraints weight = 4402.420| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.6361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5643 Z= 0.158 Angle : 0.628 10.027 7665 Z= 0.296 Chirality : 0.041 0.170 875 Planarity : 0.003 0.034 941 Dihedral : 3.699 16.685 729 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 5.26 % Allowed : 23.19 % Favored : 71.55 % 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: 0.36 (0.34), residues: 671 helix: 1.54 (0.27), residues: 406 sheet: -0.27 (1.30), residues: 17 loop : -2.03 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 131 HIS 0.005 0.001 HIS A 213 PHE 0.042 0.001 PHE A 529 TYR 0.021 0.001 TYR A 559 ARG 0.002 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.4572 (ptm160) cc_final: 0.4038 (tpt170) REVERT: A 270 ILE cc_start: 0.8365 (mm) cc_final: 0.8030 (mm) REVERT: A 427 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7037 (t80) REVERT: A 496 SER cc_start: 0.9087 (m) cc_final: 0.8641 (p) outliers start: 32 outliers final: 24 residues processed: 113 average time/residue: 0.1283 time to fit residues: 20.5069 Evaluate side-chains 109 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 0.0270 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** 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 = 0.4093 r_free = 0.4093 target = 0.139554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.109145 restraints weight = 13758.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.112895 restraints weight = 6909.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.115310 restraints weight = 4423.993| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.6744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5643 Z= 0.166 Angle : 0.628 9.656 7665 Z= 0.297 Chirality : 0.040 0.170 875 Planarity : 0.003 0.034 941 Dihedral : 3.711 18.414 729 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.95 % Allowed : 23.52 % Favored : 72.53 % 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: 0.42 (0.34), residues: 671 helix: 1.55 (0.27), residues: 407 sheet: 0.12 (1.34), residues: 17 loop : -1.96 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 473 HIS 0.004 0.001 HIS A 213 PHE 0.045 0.001 PHE A 529 TYR 0.017 0.001 TYR A 559 ARG 0.002 0.000 ARG A 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 74 ARG cc_start: 0.4223 (ptm160) cc_final: 0.3892 (tpt170) REVERT: A 270 ILE cc_start: 0.8406 (mm) cc_final: 0.8093 (mm) REVERT: A 427 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.6945 (t80) REVERT: A 496 SER cc_start: 0.8951 (m) cc_final: 0.8526 (p) outliers start: 24 outliers final: 22 residues processed: 104 average time/residue: 0.1313 time to fit residues: 19.4017 Evaluate side-chains 108 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 30 optimal weight: 0.0060 chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 0.0770 chunk 54 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 overall best weight: 0.4954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.139865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.109856 restraints weight = 13635.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.113590 restraints weight = 6832.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.116022 restraints weight = 4369.217| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.6982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5643 Z= 0.158 Angle : 0.641 9.687 7665 Z= 0.301 Chirality : 0.040 0.189 875 Planarity : 0.003 0.033 941 Dihedral : 3.702 16.701 729 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.11 % Allowed : 24.67 % Favored : 71.22 % 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: 0.47 (0.34), residues: 671 helix: 1.56 (0.27), residues: 405 sheet: 0.07 (1.35), residues: 17 loop : -1.86 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 531 HIS 0.004 0.001 HIS A 213 PHE 0.046 0.001 PHE A 529 TYR 0.031 0.001 TYR A 683 ARG 0.001 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 270 ILE cc_start: 0.8421 (mm) cc_final: 0.8094 (mm) REVERT: A 427 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.6981 (t80) REVERT: A 496 SER cc_start: 0.8941 (m) cc_final: 0.8523 (p) REVERT: A 585 MET cc_start: 0.1906 (tmm) cc_final: 0.0393 (mmt) outliers start: 25 outliers final: 22 residues processed: 103 average time/residue: 0.1203 time to fit residues: 17.8535 Evaluate side-chains 104 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 0.9980 chunk 41 optimal weight: 0.0170 chunk 57 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 0.0470 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 0.0470 chunk 46 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 0.0050 overall best weight: 0.1428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.142736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.113033 restraints weight = 13806.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.116955 restraints weight = 6807.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.119420 restraints weight = 4278.620| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.6956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5643 Z= 0.138 Angle : 0.665 10.927 7665 Z= 0.309 Chirality : 0.040 0.237 875 Planarity : 0.003 0.033 941 Dihedral : 3.693 18.178 729 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.12 % Allowed : 24.67 % Favored : 72.20 % Cbeta Deviations : 0.15 % 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: 0.50 (0.35), residues: 671 helix: 1.60 (0.27), residues: 404 sheet: 0.06 (1.33), residues: 17 loop : -1.86 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 531 HIS 0.003 0.001 HIS A 213 PHE 0.048 0.001 PHE A 529 TYR 0.011 0.001 TYR A 203 ARG 0.002 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 270 ILE cc_start: 0.8414 (mm) cc_final: 0.8081 (mm) REVERT: A 496 SER cc_start: 0.8848 (m) cc_final: 0.8463 (p) REVERT: A 585 MET cc_start: 0.2080 (tmm) cc_final: 0.0548 (mmt) REVERT: A 627 THR cc_start: 0.7533 (m) cc_final: 0.6923 (p) outliers start: 19 outliers final: 16 residues processed: 102 average time/residue: 0.1264 time to fit residues: 19.0371 Evaluate side-chains 100 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 25 optimal weight: 0.0770 chunk 4 optimal weight: 0.0570 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.140320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.110660 restraints weight = 13871.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.114446 restraints weight = 6858.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.116887 restraints weight = 4336.953| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.7266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5643 Z= 0.158 Angle : 0.683 17.824 7665 Z= 0.318 Chirality : 0.041 0.219 875 Planarity : 0.003 0.033 941 Dihedral : 3.693 16.902 729 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.12 % Allowed : 24.67 % Favored : 72.20 % 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: 0.58 (0.35), residues: 671 helix: 1.65 (0.27), residues: 405 sheet: 0.06 (1.33), residues: 17 loop : -1.82 (0.42), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 531 HIS 0.004 0.001 HIS A 213 PHE 0.047 0.001 PHE A 529 TYR 0.021 0.001 TYR A 33 ARG 0.002 0.000 ARG A 326 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 ILE cc_start: 0.8459 (mm) cc_final: 0.8132 (mm) REVERT: A 496 SER cc_start: 0.8866 (m) cc_final: 0.8466 (p) REVERT: A 585 MET cc_start: 0.2214 (tmm) cc_final: 0.0715 (mmt) outliers start: 19 outliers final: 17 residues processed: 97 average time/residue: 0.1078 time to fit residues: 15.6635 Evaluate side-chains 103 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 9 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.135712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.105641 restraints weight = 13996.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.109210 restraints weight = 6975.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.111636 restraints weight = 4459.200| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.8030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5643 Z= 0.200 Angle : 0.699 15.520 7665 Z= 0.330 Chirality : 0.042 0.226 875 Planarity : 0.004 0.034 941 Dihedral : 3.962 18.103 729 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.45 % Allowed : 24.34 % Favored : 72.20 % 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: 0.42 (0.34), residues: 671 helix: 1.54 (0.27), residues: 407 sheet: -0.75 (1.55), residues: 12 loop : -1.85 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 531 HIS 0.005 0.001 HIS A 213 PHE 0.045 0.001 PHE A 529 TYR 0.022 0.002 TYR A 33 ARG 0.002 0.000 ARG A 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1982.20 seconds wall clock time: 36 minutes 19.08 seconds (2179.08 seconds total)