Starting phenix.real_space_refine on Thu Mar 13 14:09:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8axa_15697/03_2025/8axa_15697.cif Found real_map, /net/cci-nas-00/data/ceres_data/8axa_15697/03_2025/8axa_15697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8axa_15697/03_2025/8axa_15697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8axa_15697/03_2025/8axa_15697.map" model { file = "/net/cci-nas-00/data/ceres_data/8axa_15697/03_2025/8axa_15697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8axa_15697/03_2025/8axa_15697.cif" } resolution = 2.96 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= 0.025 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 P 251 5.49 5 S 11 5.16 5 C 4801 2.51 5 N 1637 2.21 5 O 2442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9142 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3774 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 17, 'TRANS': 447} Chain breaks: 1 Chain: "B" Number of atoms: 5000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 5000 Inner-chain residues flagged as termini: ['pdbres=" U B 244 "'] Classifications: {'RNA': 235} Modifications used: {'5*END': 2, 'rna2p_pur': 18, 'rna2p_pyr': 20, 'rna3p_pur': 103, 'rna3p_pyr': 94} Link IDs: {'rna2p': 38, 'rna3p': 196} Chain: "C" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 261 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 104 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 7.14, per 1000 atoms: 0.78 Number of scatterers: 9142 At special positions: 0 Unit cell: (113.984, 94.016, 122.304, 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) S 11 16.00 P 251 15.00 O 2442 8.00 N 1637 7.00 C 4801 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: 2.54 Conformation dependent library (CDL) restraints added in 563.3 milliseconds 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 878 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 2 sheets defined 55.5% alpha, 10.1% beta 84 base pairs and 121 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'A' and resid 13 through 28 removed outlier: 3.711A pdb=" N ASP A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 42 Processing helix chain 'A' and resid 44 through 52 Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.831A pdb=" N ALA A 73 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 98 Processing helix chain 'A' and resid 321 through 338 removed outlier: 3.675A pdb=" N PHE A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 382 Processing helix chain 'A' and resid 384 through 406 Processing helix chain 'A' and resid 414 through 429 Processing helix chain 'A' and resid 476 through 482 Processing helix chain 'A' and resid 485 through 505 removed outlier: 3.874A pdb=" N ASN A 489 " --> pdb=" O TYR A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 538 Processing helix chain 'A' and resid 547 through 567 removed outlier: 3.535A pdb=" N MET A 551 " --> pdb=" O LYS A 547 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU A 553 " --> pdb=" O GLY A 549 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 559 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN A 560 " --> pdb=" O GLN A 556 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 585 Processing helix chain 'A' and resid 589 through 605 removed outlier: 3.671A pdb=" N ILE A 594 " --> pdb=" O TYR A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 637 removed outlier: 3.875A pdb=" N THR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG A 637 " --> pdb=" O LEU A 633 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 284 through 285 removed outlier: 3.541A pdb=" N GLY A 352 " --> pdb=" O PHE A 285 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN A 351 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU A 371 " --> pdb=" O LEU A 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 471 through 475 removed outlier: 6.638A pdb=" N VAL A 463 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR A 474 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 461 " --> pdb=" O TYR A 474 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE A 447 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N VAL A 544 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL A 449 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N VAL A 451 " --> pdb=" O PRO A 546 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE A 543 " --> pdb=" O GLU A 609 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLY A 611 " --> pdb=" O ILE A 543 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU A 545 " --> pdb=" O GLY A 611 " (cutoff:3.500A) 200 hydrogen bonds defined for protein. 588 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 220 hydrogen bonds 416 hydrogen bond angles 0 basepair planarities 84 basepair parallelities 121 stacking parallelities Total time for adding SS restraints: 4.04 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1579 1.33 - 1.45: 3697 1.45 - 1.57: 4054 1.57 - 1.69: 500 1.69 - 1.80: 16 Bond restraints: 9846 Sorted by residual: bond pdb=" C3' U B 190 " pdb=" O3' U B 190 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.50e-02 4.44e+03 1.27e+00 bond pdb=" CG ARG A 493 " pdb=" CD ARG A 493 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.15e+00 bond pdb=" CB MET A 551 " pdb=" CG MET A 551 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.54e-01 bond pdb=" CB VAL A 377 " pdb=" CG1 VAL A 377 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.45e-01 bond pdb=" CB GLU A 358 " pdb=" CG GLU A 358 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.44e-01 ... (remaining 9841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 14284 1.88 - 3.76: 212 3.76 - 5.64: 19 5.64 - 7.52: 7 7.52 - 9.40: 2 Bond angle restraints: 14524 Sorted by residual: angle pdb=" C CYS A 63 " pdb=" N GLN A 64 " pdb=" CA GLN A 64 " ideal model delta sigma weight residual 120.06 125.29 -5.23 1.19e+00 7.06e-01 1.93e+01 angle pdb=" C3' U B 190 " pdb=" O3' U B 190 " pdb=" P G B 191 " ideal model delta sigma weight residual 120.20 125.48 -5.28 1.50e+00 4.44e-01 1.24e+01 angle pdb=" C THR A 68 " pdb=" N ASP A 69 " pdb=" CA ASP A 69 " ideal model delta sigma weight residual 121.98 131.38 -9.40 3.11e+00 1.03e-01 9.13e+00 angle pdb=" O3' U B 190 " pdb=" P G B 191 " pdb=" OP1 G B 191 " ideal model delta sigma weight residual 108.00 116.20 -8.20 3.00e+00 1.11e-01 7.47e+00 angle pdb=" CA GLY A 52 " pdb=" C GLY A 52 " pdb=" O GLY A 52 " ideal model delta sigma weight residual 122.24 120.06 2.18 8.70e-01 1.32e+00 6.26e+00 ... (remaining 14519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.46: 5252 30.46 - 60.92: 712 60.92 - 91.38: 210 91.38 - 121.84: 8 121.84 - 152.30: 3 Dihedral angle restraints: 6185 sinusoidal: 4829 harmonic: 1356 Sorted by residual: dihedral pdb=" CA LEU A 62 " pdb=" C LEU A 62 " pdb=" N CYS A 63 " pdb=" CA CYS A 63 " ideal model delta harmonic sigma weight residual 180.00 159.37 20.63 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" C4' U B 190 " pdb=" C3' U B 190 " pdb=" O3' U B 190 " pdb=" P G B 191 " ideal model delta sinusoidal sigma weight residual -110.00 42.30 -152.30 1 3.50e+01 8.16e-04 1.48e+01 dihedral pdb=" CA PHE A 433 " pdb=" C PHE A 433 " pdb=" N GLU A 434 " pdb=" CA GLU A 434 " ideal model delta harmonic sigma weight residual 180.00 160.98 19.02 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 6182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1445 0.037 - 0.074: 287 0.074 - 0.110: 60 0.110 - 0.147: 13 0.147 - 0.184: 5 Chirality restraints: 1810 Sorted by residual: chirality pdb=" CB ILE A 4 " pdb=" CA ILE A 4 " pdb=" CG1 ILE A 4 " pdb=" CG2 ILE A 4 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" C1' A B 139 " pdb=" O4' A B 139 " pdb=" C2' A B 139 " pdb=" N9 A B 139 " both_signs ideal model delta sigma weight residual False 2.46 2.28 0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" C3' G B 29 " pdb=" C4' G B 29 " pdb=" O3' G B 29 " pdb=" C2' G B 29 " both_signs ideal model delta sigma weight residual False -2.48 -2.30 -0.17 2.00e-01 2.50e+01 7.44e-01 ... (remaining 1807 not shown) Planarity restraints: 923 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 64 " 0.058 5.00e-02 4.00e+02 8.82e-02 1.25e+01 pdb=" N PRO A 65 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO A 65 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 65 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G B 49 " 0.029 2.00e-02 2.50e+03 1.25e-02 4.68e+00 pdb=" N9 G B 49 " -0.031 2.00e-02 2.50e+03 pdb=" C8 G B 49 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G B 49 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B 49 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G B 49 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G B 49 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G B 49 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G B 49 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G B 49 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G B 49 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G B 49 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 139 " -0.023 2.00e-02 2.50e+03 1.15e-02 3.63e+00 pdb=" N9 A B 139 " 0.030 2.00e-02 2.50e+03 pdb=" C8 A B 139 " -0.000 2.00e-02 2.50e+03 pdb=" N7 A B 139 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A B 139 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A B 139 " -0.001 2.00e-02 2.50e+03 pdb=" N6 A B 139 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A B 139 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A B 139 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A B 139 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A B 139 " -0.001 2.00e-02 2.50e+03 ... (remaining 920 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 517 2.69 - 3.25: 8356 3.25 - 3.80: 17762 3.80 - 4.35: 22141 4.35 - 4.90: 30956 Nonbonded interactions: 79732 Sorted by model distance: nonbonded pdb=" O GLY A 454 " pdb=" OH TYR A 590 " model vdw 2.143 3.040 nonbonded pdb=" OE2 GLU A 34 " pdb=" O HOH A 701 " model vdw 2.176 3.040 nonbonded pdb=" O2' A B 63 " pdb=" O3' G B 88 " model vdw 2.193 3.040 nonbonded pdb=" O2' A B 169 " pdb=" N6 A B 173 " model vdw 2.232 3.120 nonbonded pdb=" O4 U B 144 " pdb=" N4 C B 148 " model vdw 2.234 3.120 ... (remaining 79727 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.550 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 29.050 Find NCS groups from input model: 0.070 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:12.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 : 0.003 0.032 9846 Z= 0.205 Angle : 0.571 9.396 14524 Z= 0.294 Chirality : 0.033 0.184 1810 Planarity : 0.006 0.088 923 Dihedral : 23.946 152.304 5307 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.49 % Allowed : 32.28 % Favored : 67.23 % 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: 0.01 (0.41), residues: 461 helix: 1.25 (0.32), residues: 239 sheet: -1.71 (0.59), residues: 80 loop : -0.95 (0.59), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 366 HIS 0.004 0.001 HIS A 323 PHE 0.012 0.002 PHE A 401 TYR 0.026 0.002 TYR A 497 ARG 0.011 0.001 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.637 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 46 average time/residue: 1.2269 time to fit residues: 61.0005 Evaluate side-chains 27 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 75 GLN A 367 ASN A 420 GLN A 580 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.114125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.090077 restraints weight = 26916.330| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.87 r_work: 0.3603 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9846 Z= 0.199 Angle : 0.561 8.443 14524 Z= 0.287 Chirality : 0.032 0.228 1810 Planarity : 0.005 0.088 923 Dihedral : 23.884 152.264 4347 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.88 % Allowed : 32.52 % Favored : 63.59 % 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: -0.10 (0.40), residues: 461 helix: 1.03 (0.31), residues: 254 sheet: -1.73 (0.60), residues: 76 loop : -1.01 (0.60), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 366 HIS 0.003 0.001 HIS A 342 PHE 0.010 0.001 PHE A 433 TYR 0.019 0.002 TYR A 590 ARG 0.004 0.001 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 33 time to evaluate : 0.680 Fit side-chains REVERT: A 44 ASP cc_start: 0.9161 (OUTLIER) cc_final: 0.8543 (t0) REVERT: A 420 GLN cc_start: 0.6245 (OUTLIER) cc_final: 0.5954 (tm-30) REVERT: A 590 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.7943 (m-10) outliers start: 16 outliers final: 2 residues processed: 44 average time/residue: 1.1544 time to fit residues: 55.5590 Evaluate side-chains 33 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 420 GLN Chi-restraints excluded: chain A residue 590 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.112730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.088165 restraints weight = 27308.964| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.87 r_work: 0.3569 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9846 Z= 0.277 Angle : 0.600 8.797 14524 Z= 0.306 Chirality : 0.034 0.230 1810 Planarity : 0.005 0.085 923 Dihedral : 23.932 151.018 4347 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 7.04 % Allowed : 29.37 % Favored : 63.59 % 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: -0.37 (0.40), residues: 461 helix: 0.78 (0.31), residues: 255 sheet: -1.85 (0.61), residues: 76 loop : -1.06 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 366 HIS 0.005 0.001 HIS A 323 PHE 0.013 0.001 PHE A 433 TYR 0.019 0.002 TYR A 590 ARG 0.006 0.001 ARG A 435 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 29 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7636 (tm) REVERT: A 44 ASP cc_start: 0.9184 (OUTLIER) cc_final: 0.8582 (t0) REVERT: A 385 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: A 590 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.8227 (m-10) outliers start: 29 outliers final: 7 residues processed: 53 average time/residue: 0.7555 time to fit residues: 44.9433 Evaluate side-chains 36 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 629 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 379 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.112101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.087381 restraints weight = 27056.730| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.89 r_work: 0.3556 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9846 Z= 0.271 Angle : 0.594 9.128 14524 Z= 0.303 Chirality : 0.034 0.226 1810 Planarity : 0.005 0.081 923 Dihedral : 23.945 149.533 4347 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 6.55 % Allowed : 30.83 % Favored : 62.62 % 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 (0.40), residues: 461 helix: 0.89 (0.31), residues: 254 sheet: -1.91 (0.61), residues: 76 loop : -0.96 (0.60), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 366 HIS 0.004 0.001 HIS A 323 PHE 0.014 0.001 PHE A 433 TYR 0.020 0.002 TYR A 590 ARG 0.005 0.001 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 28 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7654 (tm) REVERT: A 44 ASP cc_start: 0.9152 (OUTLIER) cc_final: 0.8508 (t0) REVERT: A 385 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7717 (mp0) REVERT: A 397 GLU cc_start: 0.4420 (OUTLIER) cc_final: 0.3700 (tm-30) outliers start: 27 outliers final: 11 residues processed: 51 average time/residue: 0.7652 time to fit residues: 44.3332 Evaluate side-chains 39 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 24 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 629 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 66 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 26 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.110801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.085869 restraints weight = 26999.974| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.88 r_work: 0.3534 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9846 Z= 0.321 Angle : 0.637 9.491 14524 Z= 0.323 Chirality : 0.036 0.223 1810 Planarity : 0.005 0.079 923 Dihedral : 24.014 147.706 4347 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 6.80 % Allowed : 31.07 % Favored : 62.14 % 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: -0.32 (0.40), residues: 461 helix: 0.91 (0.31), residues: 253 sheet: -1.96 (0.61), residues: 76 loop : -1.11 (0.60), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 366 HIS 0.005 0.001 HIS A 323 PHE 0.014 0.002 PHE A 433 TYR 0.023 0.002 TYR A 590 ARG 0.005 0.001 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 26 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7737 (tm) REVERT: A 44 ASP cc_start: 0.9135 (OUTLIER) cc_final: 0.8501 (t0) REVERT: A 385 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7726 (mp0) REVERT: A 397 GLU cc_start: 0.4443 (OUTLIER) cc_final: 0.3718 (tm-30) outliers start: 28 outliers final: 13 residues processed: 51 average time/residue: 0.7636 time to fit residues: 43.8566 Evaluate side-chains 41 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 24 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 484 ASN Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 629 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 5 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 11 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 75 GLN A 379 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.113617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.089355 restraints weight = 27040.221| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.82 r_work: 0.3624 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9846 Z= 0.171 Angle : 0.562 9.514 14524 Z= 0.284 Chirality : 0.032 0.218 1810 Planarity : 0.005 0.079 923 Dihedral : 23.896 147.272 4347 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 5.34 % Allowed : 33.25 % Favored : 61.41 % 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: 0.21 (0.41), residues: 461 helix: 1.50 (0.32), residues: 242 sheet: -1.86 (0.59), residues: 82 loop : -0.90 (0.59), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 588 HIS 0.002 0.001 HIS A 342 PHE 0.012 0.001 PHE A 433 TYR 0.011 0.001 TYR A 474 ARG 0.005 0.001 ARG A 435 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 25 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7726 (tm) REVERT: A 44 ASP cc_start: 0.9142 (OUTLIER) cc_final: 0.8490 (t0) REVERT: A 385 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: A 514 PHE cc_start: 0.6197 (OUTLIER) cc_final: 0.5686 (p90) outliers start: 22 outliers final: 11 residues processed: 45 average time/residue: 0.7958 time to fit residues: 40.5080 Evaluate side-chains 37 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 22 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 514 PHE Chi-restraints excluded: chain A residue 629 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 25 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.110763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.086328 restraints weight = 27585.111| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.86 r_work: 0.3544 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9846 Z= 0.378 Angle : 0.686 15.596 14524 Z= 0.341 Chirality : 0.037 0.225 1810 Planarity : 0.006 0.078 923 Dihedral : 24.010 144.410 4347 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 5.83 % Allowed : 31.80 % Favored : 62.38 % 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: -0.33 (0.40), residues: 461 helix: 0.90 (0.31), residues: 253 sheet: -1.98 (0.61), residues: 76 loop : -1.10 (0.60), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 588 HIS 0.005 0.001 HIS A 323 PHE 0.013 0.002 PHE A 433 TYR 0.013 0.002 TYR A 474 ARG 0.006 0.001 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 28 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7761 (tm) REVERT: A 44 ASP cc_start: 0.9167 (OUTLIER) cc_final: 0.8549 (t0) REVERT: A 385 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7743 (mp0) REVERT: A 514 PHE cc_start: 0.6228 (OUTLIER) cc_final: 0.5615 (p90) outliers start: 24 outliers final: 11 residues processed: 47 average time/residue: 0.8268 time to fit residues: 43.4469 Evaluate side-chains 40 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 25 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 514 PHE Chi-restraints excluded: chain A residue 629 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 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 75 GLN A 379 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.112563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.088187 restraints weight = 27624.075| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.85 r_work: 0.3595 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9846 Z= 0.201 Angle : 0.591 12.480 14524 Z= 0.297 Chirality : 0.033 0.216 1810 Planarity : 0.005 0.078 923 Dihedral : 23.923 143.153 4347 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 5.58 % Allowed : 32.28 % Favored : 62.14 % 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: 0.24 (0.41), residues: 461 helix: 1.48 (0.31), residues: 240 sheet: -1.88 (0.59), residues: 82 loop : -0.73 (0.61), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 588 HIS 0.003 0.001 HIS A 323 PHE 0.013 0.001 PHE A 433 TYR 0.016 0.002 TYR A 590 ARG 0.004 0.000 ARG A 435 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 25 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7827 (tm) REVERT: A 44 ASP cc_start: 0.9138 (OUTLIER) cc_final: 0.8504 (t0) REVERT: A 385 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: A 514 PHE cc_start: 0.6279 (OUTLIER) cc_final: 0.5652 (p90) outliers start: 23 outliers final: 12 residues processed: 46 average time/residue: 0.8244 time to fit residues: 42.2876 Evaluate side-chains 38 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 22 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 514 PHE Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 629 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 22 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.110799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.086767 restraints weight = 27018.692| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.77 r_work: 0.3593 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 9846 Z= 0.322 Angle : 0.660 13.408 14524 Z= 0.328 Chirality : 0.036 0.273 1810 Planarity : 0.005 0.078 923 Dihedral : 23.964 140.584 4347 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.85 % Allowed : 33.25 % Favored : 61.89 % 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: -0.25 (0.40), residues: 461 helix: 0.95 (0.31), residues: 253 sheet: -1.98 (0.62), residues: 76 loop : -1.04 (0.60), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 588 HIS 0.005 0.001 HIS A 323 PHE 0.013 0.002 PHE A 433 TYR 0.026 0.002 TYR A 497 ARG 0.005 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 24 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7818 (tm) REVERT: A 44 ASP cc_start: 0.9172 (OUTLIER) cc_final: 0.8550 (t0) REVERT: A 385 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7840 (mp0) outliers start: 20 outliers final: 12 residues processed: 42 average time/residue: 0.7749 time to fit residues: 36.8662 Evaluate side-chains 37 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 22 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 629 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 66 optimal weight: 6.9990 chunk 44 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.112798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.088800 restraints weight = 27766.115| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.79 r_work: 0.3638 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9846 Z= 0.195 Angle : 0.594 13.271 14524 Z= 0.295 Chirality : 0.033 0.321 1810 Planarity : 0.005 0.078 923 Dihedral : 23.869 140.115 4347 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.85 % Allowed : 33.01 % Favored : 62.14 % 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: 0.16 (0.41), residues: 461 helix: 1.46 (0.31), residues: 242 sheet: -1.87 (0.59), residues: 82 loop : -0.94 (0.59), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 588 HIS 0.003 0.001 HIS A 323 PHE 0.012 0.001 PHE A 433 TYR 0.026 0.002 TYR A 497 ARG 0.004 0.000 ARG A 435 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 21 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7853 (tm) REVERT: A 44 ASP cc_start: 0.9153 (OUTLIER) cc_final: 0.8528 (t0) outliers start: 20 outliers final: 12 residues processed: 38 average time/residue: 0.7792 time to fit residues: 33.4078 Evaluate side-chains 35 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 21 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 629 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 379 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.110803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.086715 restraints weight = 27017.237| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.78 r_work: 0.3581 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 9846 Z= 0.332 Angle : 0.672 13.175 14524 Z= 0.334 Chirality : 0.036 0.259 1810 Planarity : 0.005 0.078 923 Dihedral : 23.947 141.128 4347 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 4.85 % Allowed : 32.52 % Favored : 62.62 % 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: -0.30 (0.40), residues: 461 helix: 0.94 (0.31), residues: 253 sheet: -2.01 (0.62), residues: 76 loop : -1.09 (0.59), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 588 HIS 0.005 0.001 HIS A 323 PHE 0.014 0.002 PHE A 514 TYR 0.026 0.002 TYR A 497 ARG 0.004 0.000 ARG A 350 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5564.12 seconds wall clock time: 96 minutes 47.25 seconds (5807.25 seconds total)