Starting phenix.real_space_refine on Thu Mar 6 06:35:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ppj_13581/03_2025/7ppj_13581.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ppj_13581/03_2025/7ppj_13581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ppj_13581/03_2025/7ppj_13581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ppj_13581/03_2025/7ppj_13581.map" model { file = "/net/cci-nas-00/data/ceres_data/7ppj_13581/03_2025/7ppj_13581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ppj_13581/03_2025/7ppj_13581.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.081 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 3304 2.51 5 N 893 2.21 5 O 940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5175 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5174 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 643, 5157 Classifications: {'peptide': 643} Link IDs: {'PTRANS': 27, 'TRANS': 615} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 643, 5157 Classifications: {'peptide': 643} Link IDs: {'PTRANS': 27, 'TRANS': 615} Chain breaks: 2 bond proxies already assigned to first conformer: 5243 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1914 SG CYS A 268 27.819 26.355 48.835 1.00 67.67 S ATOM 2198 SG CYS A 303 26.980 29.739 48.695 1.00 50.58 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="ZN ZN A 901 " occ=0.83 Time building chain proxies: 6.20, per 1000 atoms: 1.20 Number of scatterers: 5175 At special positions: 0 Unit cell: (64.852, 91.002, 120.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 940 8.00 N 893 7.00 C 3304 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: 1.20 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" ND1 HIS A 266 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 303 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 268 " 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1228 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 8 sheets defined 37.3% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 32 through 54 removed outlier: 3.765A pdb=" N ASN A 52 " --> pdb=" O CYS A 48 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.553A pdb=" N ARG A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER A 84 " --> pdb=" O ILE A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 142 removed outlier: 3.539A pdb=" N GLN A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 203 through 222 Proline residue: A 213 - end of helix Processing helix chain 'A' and resid 247 through 261 Processing helix chain 'A' and resid 324 through 333 removed outlier: 3.868A pdb=" N MET A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 402 through 411 Processing helix chain 'A' and resid 424 through 430 removed outlier: 3.839A pdb=" N ASP A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 429 " --> pdb=" O TRP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 480 Processing helix chain 'A' and resid 525 through 538 removed outlier: 4.011A pdb=" N ILE A 535 " --> pdb=" O GLN A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 566 Processing helix chain 'A' and resid 582 through 599 removed outlier: 4.086A pdb=" N ARG A 590 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 604 No H-bonds generated for 'chain 'A' and resid 602 through 604' Processing helix chain 'A' and resid 612 through 621 Processing helix chain 'A' and resid 631 through 637 Processing helix chain 'A' and resid 651 through 654 Processing helix chain 'A' and resid 660 through 671 removed outlier: 3.743A pdb=" N LYS A 664 " --> pdb=" O ASP A 660 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 120 Processing sheet with id=AA3, first strand: chain 'A' and resid 197 through 198 removed outlier: 6.946A pdb=" N VAL A 283 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR A 292 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 281 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N CYS A 294 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASN A 279 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE A 296 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL A 277 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 316 Processing sheet with id=AA5, first strand: chain 'A' and resid 345 through 347 Processing sheet with id=AA6, first strand: chain 'A' and resid 385 through 387 removed outlier: 6.325A pdb=" N VAL A 386 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N PHE A 421 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS A 439 " --> pdb=" O ILE A 455 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 539 through 541 Processing sheet with id=AA8, first strand: chain 'A' and resid 573 through 575 removed outlier: 6.299A pdb=" N LEU A 607 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ASP A 649 " --> pdb=" O LEU A 607 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A 609 " --> pdb=" O ASP A 649 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 628 " --> pdb=" O ILE A 606 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR A 608 " --> pdb=" O GLN A 628 " (cutoff:3.500A) 197 hydrogen bonds defined for protein. 568 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: 1.63 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1618 1.34 - 1.45: 679 1.45 - 1.57: 2940 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 5287 Sorted by residual: bond pdb=" N THR A 222 " pdb=" CA THR A 222 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.17e-02 7.31e+03 1.01e+01 bond pdb=" N VAL A 386 " pdb=" CA VAL A 386 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.28e-02 6.10e+03 9.91e+00 bond pdb=" N ILE A 451 " pdb=" CA ILE A 451 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.91e+00 bond pdb=" N GLY A 225 " pdb=" CA GLY A 225 " ideal model delta sigma weight residual 1.446 1.474 -0.028 9.50e-03 1.11e+04 8.79e+00 bond pdb=" N ILE A 5 " pdb=" CA ILE A 5 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.22e-02 6.72e+03 8.40e+00 ... (remaining 5282 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 6755 1.44 - 2.89: 323 2.89 - 4.33: 58 4.33 - 5.78: 11 5.78 - 7.22: 2 Bond angle restraints: 7149 Sorted by residual: angle pdb=" N VAL A 7 " pdb=" CA VAL A 7 " pdb=" C VAL A 7 " ideal model delta sigma weight residual 112.83 107.38 5.45 9.90e-01 1.02e+00 3.03e+01 angle pdb=" CA GLN A 446 " pdb=" C GLN A 446 " pdb=" O GLN A 446 " ideal model delta sigma weight residual 121.56 117.28 4.28 1.09e+00 8.42e-01 1.54e+01 angle pdb=" CA VAL A 386 " pdb=" C VAL A 386 " pdb=" O VAL A 386 " ideal model delta sigma weight residual 121.72 118.20 3.52 9.60e-01 1.09e+00 1.34e+01 angle pdb=" CA HIS A 577 " pdb=" C HIS A 577 " pdb=" O HIS A 577 " ideal model delta sigma weight residual 121.55 117.82 3.73 1.06e+00 8.90e-01 1.24e+01 angle pdb=" CA THR A 9 " pdb=" C THR A 9 " pdb=" O THR A 9 " ideal model delta sigma weight residual 121.87 117.80 4.07 1.16e+00 7.43e-01 1.23e+01 ... (remaining 7144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 2859 17.04 - 34.07: 305 34.07 - 51.11: 46 51.11 - 68.14: 8 68.14 - 85.18: 7 Dihedral angle restraints: 3225 sinusoidal: 1328 harmonic: 1897 Sorted by residual: dihedral pdb=" CA PHE A 381 " pdb=" C PHE A 381 " pdb=" N SER A 382 " pdb=" CA SER A 382 " ideal model delta harmonic sigma weight residual -180.00 -162.52 -17.48 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" C ASN A 447 " pdb=" N ASN A 447 " pdb=" CA ASN A 447 " pdb=" CB ASN A 447 " ideal model delta harmonic sigma weight residual -122.60 -130.75 8.15 0 2.50e+00 1.60e-01 1.06e+01 dihedral pdb=" CA GLN A 90 " pdb=" C GLN A 90 " pdb=" N LYS A 91 " pdb=" CA LYS A 91 " ideal model delta harmonic sigma weight residual 180.00 163.72 16.28 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 3222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 571 0.045 - 0.090: 151 0.090 - 0.134: 57 0.134 - 0.179: 13 0.179 - 0.224: 9 Chirality restraints: 801 Sorted by residual: chirality pdb=" CA ASN A 447 " pdb=" N ASN A 447 " pdb=" C ASN A 447 " pdb=" CB ASN A 447 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA VAL A 576 " pdb=" N VAL A 576 " pdb=" C VAL A 576 " pdb=" CB VAL A 576 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ILE A 5 " pdb=" N ILE A 5 " pdb=" C ILE A 5 " pdb=" CB ILE A 5 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 798 not shown) Planarity restraints: 913 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 613 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO A 614 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 614 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 614 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 108 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO A 109 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 109 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 109 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 602 " -0.025 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO A 603 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 603 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 603 " -0.022 5.00e-02 4.00e+02 ... (remaining 910 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1037 2.78 - 3.31: 5079 3.31 - 3.84: 8303 3.84 - 4.37: 9891 4.37 - 4.90: 17121 Nonbonded interactions: 41431 Sorted by model distance: nonbonded pdb=" ND2 ASN A 52 " pdb=" O TRP A 313 " model vdw 2.245 3.120 nonbonded pdb=" NZ LYS A 481 " pdb=" O GLY A 539 " model vdw 2.275 3.120 nonbonded pdb=" O LYS A 616 " pdb=" OG SER A 620 " model vdw 2.297 3.040 nonbonded pdb=" O PRO A 310 " pdb=" NE2 GLN A 322 " model vdw 2.306 3.120 nonbonded pdb=" O SER A 353 " pdb=" OG SER A 353 " model vdw 2.307 3.040 ... (remaining 41426 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 21.140 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.070 Process input model: 20.900 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 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 : 0.005 0.040 5287 Z= 0.354 Angle : 0.719 7.221 7149 Z= 0.454 Chirality : 0.054 0.224 801 Planarity : 0.004 0.042 913 Dihedral : 14.044 85.176 1997 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.75 % Favored : 92.94 % Rotamer: Outliers : 1.20 % Allowed : 3.43 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.29), residues: 642 helix: -1.57 (0.29), residues: 230 sheet: -2.24 (0.50), residues: 89 loop : -2.27 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 313 HIS 0.003 0.001 HIS A 119 PHE 0.013 0.001 PHE A 381 TYR 0.010 0.001 TYR A 608 ARG 0.002 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 MET cc_start: 0.7701 (tpt) cc_final: 0.7483 (tpp) outliers start: 5 outliers final: 1 residues processed: 107 average time/residue: 0.2478 time to fit residues: 32.4387 Evaluate side-chains 71 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 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 10 ASN A 40 ASN A 94 HIS A 182 GLN A 221 ASN ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 GLN A 512 GLN A 605 ASN A 670 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.157518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.121105 restraints weight = 25449.541| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 9.41 r_work: 0.3123 rms_B_bonded: 7.87 restraints_weight: 2.0000 r_work: 0.3289 rms_B_bonded: 5.10 restraints_weight: 4.0000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5287 Z= 0.251 Angle : 0.683 12.388 7149 Z= 0.343 Chirality : 0.047 0.172 801 Planarity : 0.004 0.053 913 Dihedral : 4.428 26.585 704 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.37 % Allowed : 12.52 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.32), residues: 642 helix: -0.38 (0.33), residues: 236 sheet: -1.87 (0.51), residues: 85 loop : -1.61 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 661 HIS 0.005 0.001 HIS A 284 PHE 0.017 0.002 PHE A 575 TYR 0.017 0.002 TYR A 183 ARG 0.004 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 LYS cc_start: 0.7910 (tptp) cc_final: 0.7707 (tptp) REVERT: A 592 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7797 (mtm) outliers start: 5 outliers final: 2 residues processed: 84 average time/residue: 0.2368 time to fit residues: 26.4714 Evaluate side-chains 71 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 592 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 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 = 0.4009 r_free = 0.4009 target = 0.157376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.120339 restraints weight = 25718.734| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 9.48 r_work: 0.3121 rms_B_bonded: 7.70 restraints_weight: 2.0000 r_work: 0.3282 rms_B_bonded: 5.06 restraints_weight: 4.0000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5287 Z= 0.256 Angle : 0.673 13.755 7149 Z= 0.333 Chirality : 0.048 0.323 801 Planarity : 0.004 0.051 913 Dihedral : 4.452 27.111 704 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.54 % Allowed : 13.04 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.32), residues: 642 helix: 0.07 (0.34), residues: 236 sheet: -1.71 (0.49), residues: 97 loop : -1.34 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 661 HIS 0.004 0.001 HIS A 284 PHE 0.015 0.002 PHE A 421 TYR 0.031 0.002 TYR A 183 ARG 0.004 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 458 LYS cc_start: 0.7953 (tptp) cc_final: 0.7728 (tptp) REVERT: A 680 TRP cc_start: 0.8555 (m100) cc_final: 0.8307 (m100) outliers start: 6 outliers final: 5 residues processed: 69 average time/residue: 0.1860 time to fit residues: 16.8473 Evaluate side-chains 65 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 494 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 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 = 0.3948 r_free = 0.3948 target = 0.154920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118276 restraints weight = 27860.461| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 10.24 r_work: 0.3050 rms_B_bonded: 7.70 restraints_weight: 2.0000 r_work: 0.3193 rms_B_bonded: 5.28 restraints_weight: 4.0000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5287 Z= 0.258 Angle : 0.686 18.537 7149 Z= 0.328 Chirality : 0.048 0.301 801 Planarity : 0.004 0.050 913 Dihedral : 4.455 27.031 704 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.89 % Allowed : 14.58 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.33), residues: 642 helix: 0.23 (0.35), residues: 236 sheet: -1.52 (0.50), residues: 97 loop : -1.20 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 661 HIS 0.003 0.001 HIS A 119 PHE 0.014 0.002 PHE A 421 TYR 0.009 0.001 TYR A 472 ARG 0.009 0.001 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 458 LYS cc_start: 0.8015 (tptp) cc_final: 0.7741 (tptp) REVERT: A 625 ASN cc_start: 0.6645 (t0) cc_final: 0.6165 (p0) outliers start: 9 outliers final: 7 residues processed: 70 average time/residue: 0.2479 time to fit residues: 24.6267 Evaluate side-chains 66 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 678 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 52 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 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 = 0.3955 r_free = 0.3955 target = 0.155385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.117934 restraints weight = 20958.649| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 8.30 r_work: 0.3108 rms_B_bonded: 6.78 restraints_weight: 2.0000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5287 Z= 0.242 Angle : 0.648 14.551 7149 Z= 0.314 Chirality : 0.046 0.217 801 Planarity : 0.004 0.049 913 Dihedral : 4.389 27.729 704 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.23 % Allowed : 14.58 % Favored : 83.19 % 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: -0.86 (0.33), residues: 642 helix: 0.32 (0.35), residues: 237 sheet: -1.20 (0.52), residues: 95 loop : -0.99 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 661 HIS 0.003 0.001 HIS A 119 PHE 0.012 0.002 PHE A 421 TYR 0.011 0.001 TYR A 183 ARG 0.006 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.793 Fit side-chains REVERT: A 458 LYS cc_start: 0.8040 (tptp) cc_final: 0.7782 (tptp) REVERT: A 526 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.7041 (ptp) REVERT: A 625 ASN cc_start: 0.6683 (t0) cc_final: 0.6235 (p0) REVERT: A 644 GLN cc_start: 0.7467 (mt0) cc_final: 0.7077 (mp10) outliers start: 10 outliers final: 6 residues processed: 74 average time/residue: 0.1939 time to fit residues: 19.5847 Evaluate side-chains 64 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 678 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 37 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 43 optimal weight: 0.0670 chunk 7 optimal weight: 2.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.155871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.118075 restraints weight = 24150.782| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 8.64 r_work: 0.3100 rms_B_bonded: 7.06 restraints_weight: 2.0000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5287 Z= 0.236 Angle : 0.640 14.351 7149 Z= 0.316 Chirality : 0.046 0.169 801 Planarity : 0.005 0.072 913 Dihedral : 4.260 17.744 702 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.23 % Allowed : 14.92 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.33), residues: 642 helix: 0.40 (0.34), residues: 237 sheet: -1.08 (0.52), residues: 95 loop : -0.97 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP A 328 HIS 0.005 0.001 HIS A 284 PHE 0.022 0.002 PHE A 136 TYR 0.011 0.001 TYR A 226 ARG 0.012 0.001 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.685 Fit side-chains REVERT: A 458 LYS cc_start: 0.7997 (tptp) cc_final: 0.7734 (tptp) REVERT: A 526 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.7042 (ptp) REVERT: A 574 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8001 (tt) REVERT: A 625 ASN cc_start: 0.6727 (t0) cc_final: 0.6252 (p0) REVERT: A 644 GLN cc_start: 0.7489 (mt0) cc_final: 0.7091 (mp10) outliers start: 10 outliers final: 5 residues processed: 71 average time/residue: 0.1815 time to fit residues: 16.7847 Evaluate side-chains 64 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 585 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 chunk 19 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 47 optimal weight: 0.0670 chunk 56 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 29 optimal weight: 0.2980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.158547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.119519 restraints weight = 17078.235| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 6.95 r_work: 0.3191 rms_B_bonded: 6.03 restraints_weight: 2.0000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5287 Z= 0.173 Angle : 0.612 14.280 7149 Z= 0.299 Chirality : 0.045 0.157 801 Planarity : 0.005 0.095 913 Dihedral : 4.130 17.972 702 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.72 % Allowed : 16.12 % Favored : 82.16 % 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 (0.33), residues: 642 helix: 0.62 (0.35), residues: 236 sheet: -1.01 (0.52), residues: 97 loop : -0.73 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP A 328 HIS 0.005 0.001 HIS A 284 PHE 0.014 0.001 PHE A 200 TYR 0.008 0.001 TYR A 183 ARG 0.010 0.001 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.622 Fit side-chains REVERT: A 136 PHE cc_start: 0.8269 (t80) cc_final: 0.8019 (t80) REVERT: A 381 PHE cc_start: 0.6024 (p90) cc_final: 0.5719 (p90) REVERT: A 458 LYS cc_start: 0.8014 (tptp) cc_final: 0.7712 (tptp) REVERT: A 526 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6817 (ptp) REVERT: A 541 LYS cc_start: 0.7975 (mptt) cc_final: 0.6883 (mtmt) REVERT: A 574 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7858 (tt) REVERT: A 625 ASN cc_start: 0.6696 (t0) cc_final: 0.6221 (p0) REVERT: A 644 GLN cc_start: 0.7378 (mt0) cc_final: 0.6994 (mp10) outliers start: 7 outliers final: 5 residues processed: 77 average time/residue: 0.1814 time to fit residues: 18.4578 Evaluate side-chains 69 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 585 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 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 = 0.3975 r_free = 0.3975 target = 0.156972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.119523 restraints weight = 28108.897| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 10.06 r_work: 0.3060 rms_B_bonded: 7.74 restraints_weight: 2.0000 r_work: 0.3219 rms_B_bonded: 5.09 restraints_weight: 4.0000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5287 Z= 0.236 Angle : 0.630 14.355 7149 Z= 0.310 Chirality : 0.045 0.151 801 Planarity : 0.004 0.048 913 Dihedral : 4.153 16.829 702 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.89 % Allowed : 17.32 % Favored : 80.79 % 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: -0.45 (0.33), residues: 642 helix: 0.56 (0.35), residues: 236 sheet: -0.89 (0.52), residues: 97 loop : -0.69 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.004 TRP A 328 HIS 0.003 0.001 HIS A 284 PHE 0.012 0.002 PHE A 306 TYR 0.008 0.001 TYR A 472 ARG 0.015 0.001 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 136 PHE cc_start: 0.8252 (t80) cc_final: 0.8047 (t80) REVERT: A 210 ASP cc_start: 0.8232 (t0) cc_final: 0.8024 (m-30) REVERT: A 381 PHE cc_start: 0.6099 (p90) cc_final: 0.5829 (p90) REVERT: A 458 LYS cc_start: 0.8032 (tptp) cc_final: 0.7722 (tptp) REVERT: A 526 MET cc_start: 0.7135 (OUTLIER) cc_final: 0.6813 (ptp) REVERT: A 574 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7949 (tt) REVERT: A 644 GLN cc_start: 0.7255 (mt0) cc_final: 0.6861 (mp10) outliers start: 8 outliers final: 6 residues processed: 70 average time/residue: 0.1798 time to fit residues: 16.5008 Evaluate side-chains 70 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 585 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 21 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 0.0770 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 0.0980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 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 = 0.3992 r_free = 0.3992 target = 0.158611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121366 restraints weight = 27527.306| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 10.65 r_work: 0.3086 rms_B_bonded: 7.81 restraints_weight: 2.0000 r_work: 0.3243 rms_B_bonded: 5.15 restraints_weight: 4.0000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5287 Z= 0.185 Angle : 0.618 14.341 7149 Z= 0.301 Chirality : 0.045 0.153 801 Planarity : 0.004 0.048 913 Dihedral : 4.026 17.450 702 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.89 % Allowed : 17.50 % Favored : 80.62 % 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: -0.26 (0.34), residues: 642 helix: 0.66 (0.35), residues: 236 sheet: -0.81 (0.56), residues: 89 loop : -0.54 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.004 TRP A 328 HIS 0.003 0.001 HIS A 284 PHE 0.026 0.002 PHE A 654 TYR 0.007 0.001 TYR A 393 ARG 0.009 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 136 PHE cc_start: 0.8207 (t80) cc_final: 0.7993 (t80) REVERT: A 210 ASP cc_start: 0.8222 (t0) cc_final: 0.8008 (m-30) REVERT: A 458 LYS cc_start: 0.7988 (tptp) cc_final: 0.7684 (tptp) REVERT: A 526 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6722 (ptp) REVERT: A 541 LYS cc_start: 0.7910 (mptt) cc_final: 0.6863 (mtmt) REVERT: A 574 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7972 (tt) REVERT: A 625 ASN cc_start: 0.6704 (t0) cc_final: 0.6210 (p0) REVERT: A 644 GLN cc_start: 0.7363 (mt0) cc_final: 0.6950 (mp10) REVERT: A 650 ASP cc_start: 0.7473 (t0) cc_final: 0.7097 (t0) outliers start: 8 outliers final: 6 residues processed: 73 average time/residue: 0.1814 time to fit residues: 17.3444 Evaluate side-chains 71 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 585 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 60 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 54 optimal weight: 0.0870 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 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 = 0.3982 r_free = 0.3982 target = 0.157753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.111093 restraints weight = 28653.059| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 7.02 r_work: 0.3161 rms_B_bonded: 6.29 restraints_weight: 2.0000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5287 Z= 0.202 Angle : 0.626 14.362 7149 Z= 0.306 Chirality : 0.045 0.152 801 Planarity : 0.004 0.048 913 Dihedral : 4.170 19.930 702 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.06 % Allowed : 17.50 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.34), residues: 642 helix: 0.66 (0.35), residues: 236 sheet: -0.78 (0.56), residues: 89 loop : -0.48 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP A 328 HIS 0.003 0.000 HIS A 284 PHE 0.024 0.002 PHE A 654 TYR 0.009 0.001 TYR A 662 ARG 0.006 0.000 ARG A 632 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 136 PHE cc_start: 0.8199 (t80) cc_final: 0.7927 (t80) REVERT: A 458 LYS cc_start: 0.8063 (tptp) cc_final: 0.7739 (tptp) REVERT: A 526 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6866 (ptp) REVERT: A 541 LYS cc_start: 0.8044 (mptt) cc_final: 0.6982 (mtmt) REVERT: A 574 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7980 (tt) REVERT: A 625 ASN cc_start: 0.6718 (t0) cc_final: 0.6226 (p0) REVERT: A 644 GLN cc_start: 0.7423 (mt0) cc_final: 0.6994 (mp10) outliers start: 9 outliers final: 6 residues processed: 72 average time/residue: 0.1701 time to fit residues: 16.4647 Evaluate side-chains 73 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 585 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 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 = 0.3987 r_free = 0.3987 target = 0.158296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.113064 restraints weight = 22540.564| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 6.24 r_work: 0.3199 rms_B_bonded: 5.76 restraints_weight: 2.0000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5287 Z= 0.191 Angle : 0.622 14.476 7149 Z= 0.302 Chirality : 0.045 0.151 801 Planarity : 0.004 0.048 913 Dihedral : 4.205 23.629 702 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.89 % Allowed : 17.67 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.34), residues: 642 helix: 0.69 (0.35), residues: 236 sheet: -0.70 (0.56), residues: 89 loop : -0.46 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP A 328 HIS 0.002 0.000 HIS A 284 PHE 0.028 0.002 PHE A 654 TYR 0.010 0.001 TYR A 662 ARG 0.007 0.000 ARG A 632 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3601.67 seconds wall clock time: 63 minutes 44.65 seconds (3824.65 seconds total)