Starting phenix.real_space_refine on Thu Jul 24 04:39:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ppj_13581/07_2025/7ppj_13581.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ppj_13581/07_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_13581/07_2025/7ppj_13581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ppj_13581/07_2025/7ppj_13581.map" model { file = "/net/cci-nas-00/data/ceres_data/7ppj_13581/07_2025/7ppj_13581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ppj_13581/07_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-5711/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: 6.14, per 1000 atoms: 1.19 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: 1.93 Conformation dependent library (CDL) restraints added in 2.7 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: 0.90 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: 2.36 Time building geometry restraints manager: 2.24 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 24.770 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.380 ------------------------------------------------------------------------------- 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 : 0.007 0.250 5290 Z= 0.347 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 Details of bonding type rmsd hydrogen bonds : bond 0.14377 ( 197) hydrogen bonds : angle 6.03842 ( 568) metal coordination : bond 0.15627 ( 3) covalent geometry : bond 0.00544 ( 5287) covalent geometry : angle 0.71889 ( 7149) *********************** 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 : 1.392 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: 0.4169 time to fit residues: 56.6342 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 : 1.022 ------------------------------------------------------------------------------- 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 5290 Z= 0.165 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 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 197) hydrogen bonds : angle 4.96284 ( 568) metal coordination : bond 0.00704 ( 3) covalent geometry : bond 0.00397 ( 5287) covalent geometry : angle 0.68319 ( 7149) *********************** 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 : 0.547 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: 0.1855 time to fit residues: 19.8551 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 : 0.559 ------------------------------------------------------------------------------- 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: 0.3980 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: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.157948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.121126 restraints weight = 25668.044| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 9.80 r_work: 0.3122 rms_B_bonded: 7.84 restraints_weight: 2.0000 r_work: 0.3289 rms_B_bonded: 5.08 restraints_weight: 4.0000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 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 = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5290 Z= 0.150 Angle : 0.663 13.835 7149 Z= 0.328 Chirality : 0.047 0.314 801 Planarity : 0.004 0.051 913 Dihedral : 4.422 27.260 704 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.54 % Allowed : 12.86 % Favored : 85.59 % 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: -1.31 (0.32), residues: 642 helix: 0.11 (0.34), residues: 236 sheet: -1.70 (0.49), residues: 97 loop : -1.31 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 661 HIS 0.004 0.001 HIS A 284 PHE 0.013 0.002 PHE A 421 TYR 0.029 0.002 TYR A 183 ARG 0.004 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 197) hydrogen bonds : angle 4.76919 ( 568) metal coordination : bond 0.00296 ( 3) covalent geometry : bond 0.00362 ( 5287) covalent geometry : angle 0.66340 ( 7149) *********************** 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 : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 458 LYS cc_start: 0.7882 (tptp) cc_final: 0.7667 (tptp) REVERT: A 680 TRP cc_start: 0.8544 (m100) cc_final: 0.8303 (m100) outliers start: 6 outliers final: 5 residues processed: 69 average time/residue: 0.1906 time to fit residues: 17.1378 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 : 0.598 ------------------------------------------------------------------------------- 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: 1.9990 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 2 optimal weight: 0.0980 chunk 52 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.156265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.119677 restraints weight = 27760.907| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 10.42 r_work: 0.3060 rms_B_bonded: 7.88 restraints_weight: 2.0000 r_work: 0.3214 rms_B_bonded: 5.27 restraints_weight: 4.0000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 5290 Z= 0.141 Angle : 0.672 17.786 7149 Z= 0.319 Chirality : 0.048 0.310 801 Planarity : 0.004 0.050 913 Dihedral : 4.343 27.538 704 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.89 % Allowed : 14.07 % Favored : 84.05 % 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: -0.98 (0.33), residues: 642 helix: 0.39 (0.35), residues: 236 sheet: -1.51 (0.50), residues: 97 loop : -1.11 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 661 HIS 0.002 0.001 HIS A 119 PHE 0.012 0.001 PHE A 421 TYR 0.009 0.001 TYR A 393 ARG 0.017 0.001 ARG A 384 Details of bonding type rmsd hydrogen bonds : bond 0.03448 ( 197) hydrogen bonds : angle 4.74910 ( 568) metal coordination : bond 0.00250 ( 3) covalent geometry : bond 0.00342 ( 5287) covalent geometry : angle 0.67178 ( 7149) *********************** 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 74 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 458 LYS cc_start: 0.7975 (tptp) cc_final: 0.7694 (tptp) REVERT: A 625 ASN cc_start: 0.6665 (t0) cc_final: 0.6194 (p0) outliers start: 8 outliers final: 6 residues processed: 72 average time/residue: 0.1772 time to fit residues: 16.9726 Evaluate side-chains 67 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.154364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.117037 restraints weight = 21015.944| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 8.37 r_work: 0.3106 rms_B_bonded: 6.62 restraints_weight: 2.0000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 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 = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5290 Z= 0.181 Angle : 0.674 14.176 7149 Z= 0.326 Chirality : 0.047 0.217 801 Planarity : 0.004 0.049 913 Dihedral : 4.423 27.158 704 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.40 % Allowed : 14.58 % Favored : 83.02 % 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: -0.95 (0.33), residues: 642 helix: 0.30 (0.35), residues: 236 sheet: -1.28 (0.55), residues: 87 loop : -1.10 (0.34), residues: 319 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 0.015 0.002 PHE A 421 TYR 0.010 0.001 TYR A 472 ARG 0.007 0.001 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 197) hydrogen bonds : angle 4.78640 ( 568) metal coordination : bond 0.00399 ( 3) covalent geometry : bond 0.00443 ( 5287) covalent geometry : angle 0.67365 ( 7149) *********************** 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 74 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 MET cc_start: 0.8458 (mtp) cc_final: 0.8185 (mpp) REVERT: A 458 LYS cc_start: 0.8090 (tptp) cc_final: 0.7861 (tptp) REVERT: A 526 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.7030 (ptp) REVERT: A 625 ASN cc_start: 0.6713 (t0) cc_final: 0.6238 (p0) outliers start: 11 outliers final: 6 residues processed: 73 average time/residue: 0.1763 time to fit residues: 17.0143 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 : 0.537 ------------------------------------------------------------------------------- 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 585 THR Chi-restraints excluded: chain A residue 634 THR 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: 0.7980 chunk 38 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.156531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.118919 restraints weight = 24011.391| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 8.66 r_work: 0.3100 rms_B_bonded: 7.30 restraints_weight: 2.0000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 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 = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5290 Z= 0.132 Angle : 0.632 13.866 7149 Z= 0.308 Chirality : 0.045 0.164 801 Planarity : 0.005 0.070 913 Dihedral : 4.161 17.815 702 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.72 % Allowed : 15.61 % Favored : 82.68 % 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: -0.62 (0.33), residues: 642 helix: 0.52 (0.35), residues: 237 sheet: -0.99 (0.56), residues: 84 loop : -0.90 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP A 328 HIS 0.003 0.001 HIS A 265 PHE 0.020 0.002 PHE A 654 TYR 0.014 0.001 TYR A 226 ARG 0.019 0.001 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03297 ( 197) hydrogen bonds : angle 4.68876 ( 568) metal coordination : bond 0.00225 ( 3) covalent geometry : bond 0.00317 ( 5287) covalent geometry : angle 0.63220 ( 7149) *********************** 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 71 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 333 MET cc_start: 0.8427 (mtp) cc_final: 0.8072 (mpp) REVERT: A 458 LYS cc_start: 0.8054 (tptp) cc_final: 0.7791 (tptp) REVERT: A 526 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.7032 (ptp) REVERT: A 574 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7948 (tt) REVERT: A 625 ASN cc_start: 0.6713 (t0) cc_final: 0.6253 (p0) REVERT: A 644 GLN cc_start: 0.7505 (mt0) cc_final: 0.7116 (mp10) outliers start: 7 outliers final: 3 residues processed: 70 average time/residue: 0.1844 time to fit residues: 17.0220 Evaluate side-chains 63 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 56 optimal weight: 0.0070 chunk 45 optimal weight: 0.6980 chunk 33 optimal weight: 0.0870 chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 overall best weight: 0.4176 ------------------------------------------------------------------------------- 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 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 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 = 0.3988 r_free = 0.3988 target = 0.158244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.119534 restraints weight = 17149.501| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 7.01 r_work: 0.3190 rms_B_bonded: 6.05 restraints_weight: 2.0000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5290 Z= 0.114 Angle : 0.606 13.561 7149 Z= 0.295 Chirality : 0.044 0.150 801 Planarity : 0.004 0.048 913 Dihedral : 4.021 17.767 702 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.54 % Allowed : 16.12 % Favored : 82.33 % 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: -0.38 (0.33), residues: 642 helix: 0.69 (0.35), residues: 236 sheet: -0.88 (0.56), residues: 87 loop : -0.71 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP A 328 HIS 0.011 0.001 HIS A 284 PHE 0.022 0.002 PHE A 136 TYR 0.008 0.001 TYR A 183 ARG 0.009 0.001 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 197) hydrogen bonds : angle 4.64305 ( 568) metal coordination : bond 0.00143 ( 3) covalent geometry : bond 0.00269 ( 5287) covalent geometry : angle 0.60595 ( 7149) *********************** 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 73 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 333 MET cc_start: 0.8339 (mtp) cc_final: 0.7985 (mpp) REVERT: A 458 LYS cc_start: 0.7971 (tptp) cc_final: 0.7632 (tptp) REVERT: A 526 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6813 (ptp) REVERT: A 541 LYS cc_start: 0.8005 (mptt) cc_final: 0.6912 (mtmt) REVERT: A 574 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7944 (tt) REVERT: A 625 ASN cc_start: 0.6700 (t0) cc_final: 0.6208 (p0) REVERT: A 644 GLN cc_start: 0.7340 (mt0) cc_final: 0.6962 (mp10) outliers start: 6 outliers final: 4 residues processed: 72 average time/residue: 0.2094 time to fit residues: 19.6891 Evaluate side-chains 69 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.155806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.118951 restraints weight = 28129.507| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 9.91 r_work: 0.3062 rms_B_bonded: 7.69 restraints_weight: 2.0000 r_work: 0.3213 rms_B_bonded: 5.09 restraints_weight: 4.0000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5290 Z= 0.160 Angle : 0.629 13.896 7149 Z= 0.308 Chirality : 0.045 0.148 801 Planarity : 0.004 0.047 913 Dihedral : 4.133 16.664 702 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.89 % Allowed : 16.81 % Favored : 81.30 % 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: -0.44 (0.33), residues: 642 helix: 0.59 (0.35), residues: 236 sheet: -0.86 (0.56), residues: 87 loop : -0.72 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 328 HIS 0.005 0.001 HIS A 284 PHE 0.014 0.002 PHE A 306 TYR 0.009 0.001 TYR A 472 ARG 0.008 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03312 ( 197) hydrogen bonds : angle 4.66286 ( 568) metal coordination : bond 0.00340 ( 3) covalent geometry : bond 0.00393 ( 5287) covalent geometry : angle 0.62860 ( 7149) *********************** 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 71 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 458 LYS cc_start: 0.8009 (tptp) cc_final: 0.7721 (tptp) REVERT: A 526 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6895 (ptp) REVERT: A 574 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7991 (tt) REVERT: A 644 GLN cc_start: 0.7365 (mt0) cc_final: 0.6988 (mp10) outliers start: 8 outliers final: 6 residues processed: 69 average time/residue: 0.1936 time to fit residues: 17.3697 Evaluate side-chains 69 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 21 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ** 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 = 0.3959 r_free = 0.3959 target = 0.155755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.118919 restraints weight = 27707.705| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 9.85 r_work: 0.3071 rms_B_bonded: 7.60 restraints_weight: 2.0000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5290 Z= 0.151 Angle : 0.632 14.347 7149 Z= 0.309 Chirality : 0.045 0.151 801 Planarity : 0.004 0.047 913 Dihedral : 4.135 17.191 702 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.06 % Allowed : 16.81 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.33), residues: 642 helix: 0.56 (0.35), residues: 236 sheet: -0.81 (0.56), residues: 86 loop : -0.70 (0.34), residues: 320 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 0.012 0.002 PHE A 200 TYR 0.008 0.001 TYR A 472 ARG 0.007 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03292 ( 197) hydrogen bonds : angle 4.66222 ( 568) metal coordination : bond 0.00288 ( 3) covalent geometry : bond 0.00370 ( 5287) covalent geometry : angle 0.63209 ( 7149) *********************** 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 74 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 458 LYS cc_start: 0.8132 (tptp) cc_final: 0.7826 (tptp) REVERT: A 526 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.7019 (ptp) REVERT: A 574 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7985 (tt) REVERT: A 644 GLN cc_start: 0.7459 (mt0) cc_final: 0.7059 (mp10) outliers start: 9 outliers final: 7 residues processed: 72 average time/residue: 0.1952 time to fit residues: 18.4021 Evaluate side-chains 72 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 127 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 60 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** 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 = 0.3974 r_free = 0.3974 target = 0.157157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.120479 restraints weight = 28766.659| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 10.10 r_work: 0.3071 rms_B_bonded: 7.87 restraints_weight: 2.0000 r_work: 0.3225 rms_B_bonded: 5.23 restraints_weight: 4.0000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 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 = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5290 Z= 0.132 Angle : 0.636 14.608 7149 Z= 0.308 Chirality : 0.045 0.153 801 Planarity : 0.004 0.047 913 Dihedral : 4.081 17.369 702 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.72 % Allowed : 17.67 % 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: -0.28 (0.33), residues: 642 helix: 0.62 (0.35), residues: 236 sheet: -0.60 (0.56), residues: 87 loop : -0.60 (0.35), residues: 319 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 0.011 0.001 PHE A 306 TYR 0.007 0.001 TYR A 183 ARG 0.006 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03221 ( 197) hydrogen bonds : angle 4.60010 ( 568) metal coordination : bond 0.00223 ( 3) covalent geometry : bond 0.00321 ( 5287) covalent geometry : angle 0.63567 ( 7149) ********************** 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 73 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 PHE cc_start: 0.7446 (m-10) cc_final: 0.7237 (m-10) REVERT: A 210 ASP cc_start: 0.8240 (t0) cc_final: 0.8031 (m-30) REVERT: A 411 MET cc_start: 0.6878 (tpp) cc_final: 0.6600 (tpt) REVERT: A 458 LYS cc_start: 0.8048 (tptp) cc_final: 0.7759 (tptp) REVERT: A 574 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7986 (tt) REVERT: A 644 GLN cc_start: 0.7325 (mt0) cc_final: 0.6947 (mp10) outliers start: 7 outliers final: 6 residues processed: 72 average time/residue: 0.1915 time to fit residues: 17.8775 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 : 0.598 ------------------------------------------------------------------------------- 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 141 THR Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 494 VAL 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: 4.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 0.1980 chunk 49 optimal weight: 0.0670 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 ** 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 = 0.3974 r_free = 0.3974 target = 0.157086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.119783 restraints weight = 22561.223| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 8.18 r_work: 0.3120 rms_B_bonded: 7.07 restraints_weight: 2.0000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5290 Z= 0.129 Angle : 0.627 14.430 7149 Z= 0.304 Chirality : 0.045 0.152 801 Planarity : 0.004 0.047 913 Dihedral : 4.029 17.548 702 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.72 % Allowed : 18.35 % Favored : 79.93 % 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 (0.33), residues: 642 helix: 0.68 (0.35), residues: 236 sheet: -0.59 (0.56), residues: 87 loop : -0.58 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP A 328 HIS 0.002 0.001 HIS A 284 PHE 0.011 0.001 PHE A 267 TYR 0.008 0.001 TYR A 183 ARG 0.006 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03173 ( 197) hydrogen bonds : angle 4.57758 ( 568) metal coordination : bond 0.00202 ( 3) covalent geometry : bond 0.00312 ( 5287) covalent geometry : angle 0.62680 ( 7149) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3581.68 seconds wall clock time: 62 minutes 30.28 seconds (3750.28 seconds total)