Starting phenix.real_space_refine on Sat Dec 28 18:52:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8axa_15697/12_2024/8axa_15697.cif Found real_map, /net/cci-nas-00/data/ceres_data/8axa_15697/12_2024/8axa_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_15697/12_2024/8axa_15697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8axa_15697/12_2024/8axa_15697.map" model { file = "/net/cci-nas-00/data/ceres_data/8axa_15697/12_2024/8axa_15697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8axa_15697/12_2024/8axa_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-5532/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: 6.71, per 1000 atoms: 0.73 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: 2.64 Conformation dependent library (CDL) restraints added in 535.3 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: 4.13 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: 4.26 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: 3.430 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 28.430 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:11.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.010 ------------------------------------------------------------------------------- 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 : 0.670 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 46 average time/residue: 1.2484 time to fit residues: 61.8925 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 : 0.650 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 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 : 0.620 Fit side-chains REVERT: A 44 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8471 (t0) REVERT: A 420 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6945 (tm-30) REVERT: A 590 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.8007 (m-10) outliers start: 16 outliers final: 2 residues processed: 44 average time/residue: 1.0963 time to fit residues: 52.4467 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 : 0.635 ------------------------------------------------------------------------------- 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 35 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1320 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= 0.242 Angle : 0.576 8.712 14524 Z= 0.294 Chirality : 0.033 0.229 1810 Planarity : 0.005 0.084 923 Dihedral : 23.893 151.347 4347 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.37 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: -0.24 (0.40), residues: 461 helix: 0.91 (0.31), residues: 255 sheet: -1.79 (0.61), residues: 76 loop : -1.05 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 366 HIS 0.004 0.001 HIS A 323 PHE 0.013 0.001 PHE A 433 TYR 0.018 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 57 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 28 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8503 (t0) REVERT: A 455 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8535 (tt) outliers start: 29 outliers final: 7 residues processed: 52 average time/residue: 0.7114 time to fit residues: 41.8318 Evaluate side-chains 34 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 44 ASP Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 464 VAL 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 47 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9846 Z= 0.298 Angle : 0.614 9.063 14524 Z= 0.312 Chirality : 0.035 0.228 1810 Planarity : 0.005 0.081 923 Dihedral : 23.950 149.938 4347 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 6.80 % Allowed : 29.85 % Favored : 63.35 % 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: 0.80 (0.31), residues: 255 sheet: -1.94 (0.61), residues: 76 loop : -1.03 (0.61), residues: 130 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 0.001 PHE A 433 TYR 0.021 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 56 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 28 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8916 (OUTLIER) cc_final: 0.8471 (t0) REVERT: A 397 GLU cc_start: 0.5037 (OUTLIER) cc_final: 0.4444 (tm-30) REVERT: A 590 TYR cc_start: 0.8310 (OUTLIER) cc_final: 0.8086 (m-10) outliers start: 28 outliers final: 12 residues processed: 51 average time/residue: 0.6499 time to fit residues: 37.9733 Evaluate side-chains 41 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 26 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 44 ASP Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 375 CYS 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 484 ASN Chi-restraints excluded: chain A residue 590 TYR 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 0 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 A 420 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9846 Z= 0.254 Angle : 0.591 9.258 14524 Z= 0.299 Chirality : 0.034 0.223 1810 Planarity : 0.005 0.078 923 Dihedral : 23.928 148.803 4347 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 5.10 % Allowed : 31.80 % Favored : 63.11 % 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: -0.05 (0.40), residues: 461 helix: 1.15 (0.31), residues: 248 sheet: -1.88 (0.61), residues: 78 loop : -0.91 (0.59), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 588 HIS 0.004 0.001 HIS A 323 PHE 0.013 0.001 PHE A 433 TYR 0.020 0.002 TYR A 590 ARG 0.004 0.000 ARG A 435 *********************** 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 46 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 25 time to evaluate : 0.723 Fit side-chains REVERT: A 44 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8402 (t0) REVERT: A 420 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.6982 (tm-30) outliers start: 21 outliers final: 11 residues processed: 43 average time/residue: 0.7268 time to fit residues: 35.5628 Evaluate side-chains 34 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 21 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 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 420 GLN 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 629 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- 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 A 420 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1916 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= 0.238 Angle : 0.581 9.421 14524 Z= 0.294 Chirality : 0.033 0.221 1810 Planarity : 0.005 0.078 923 Dihedral : 23.915 147.957 4347 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 6.80 % Allowed : 30.58 % 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: 0.01 (0.40), residues: 461 helix: 1.22 (0.31), residues: 248 sheet: -1.88 (0.61), residues: 78 loop : -0.92 (0.59), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 588 HIS 0.004 0.001 HIS A 323 PHE 0.013 0.001 PHE A 433 TYR 0.016 0.002 TYR A 590 ARG 0.003 0.000 ARG A 350 *********************** 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 51 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 23 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8443 (t0) REVERT: A 420 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.7074 (tm-30) REVERT: A 514 PHE cc_start: 0.6453 (OUTLIER) cc_final: 0.6000 (p90) outliers start: 28 outliers final: 15 residues processed: 49 average time/residue: 0.8750 time to fit residues: 48.6085 Evaluate side-chains 41 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 23 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 29 THR Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 330 GLU 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 419 ILE Chi-restraints excluded: chain A residue 420 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 10.9990 chunk 42 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 A 420 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9846 Z= 0.172 Angle : 0.556 10.081 14524 Z= 0.278 Chirality : 0.031 0.218 1810 Planarity : 0.005 0.077 923 Dihedral : 23.845 147.023 4347 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.61 % Allowed : 33.01 % 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: 0.36 (0.41), residues: 461 helix: 1.68 (0.32), residues: 242 sheet: -1.88 (0.58), residues: 82 loop : -0.89 (0.59), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 588 HIS 0.003 0.001 HIS A 342 PHE 0.011 0.001 PHE A 433 TYR 0.011 0.001 TYR A 474 ARG 0.004 0.001 ARG A 435 *********************** 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 48 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 29 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8891 (OUTLIER) cc_final: 0.8413 (t0) REVERT: A 420 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.7295 (tm130) REVERT: A 514 PHE cc_start: 0.6290 (OUTLIER) cc_final: 0.5861 (p90) outliers start: 19 outliers final: 10 residues processed: 46 average time/residue: 0.9384 time to fit residues: 47.5356 Evaluate side-chains 36 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 23 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 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 420 GLN 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 13 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.0770 chunk 53 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 37 optimal weight: 0.3980 overall best weight: 1.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 288 ASN A 420 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9846 Z= 0.247 Angle : 0.592 9.985 14524 Z= 0.296 Chirality : 0.033 0.218 1810 Planarity : 0.005 0.077 923 Dihedral : 23.850 144.290 4347 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 5.34 % Allowed : 32.52 % 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: 0.26 (0.41), residues: 461 helix: 1.57 (0.32), residues: 242 sheet: -1.88 (0.58), residues: 82 loop : -0.88 (0.60), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 588 HIS 0.004 0.001 HIS A 323 PHE 0.013 0.001 PHE A 433 TYR 0.011 0.001 TYR A 474 ARG 0.004 0.000 ARG A 350 *********************** 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 46 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 24 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8926 (OUTLIER) cc_final: 0.8460 (t0) REVERT: A 397 GLU cc_start: 0.4940 (OUTLIER) cc_final: 0.4400 (tm-30) REVERT: A 514 PHE cc_start: 0.6304 (OUTLIER) cc_final: 0.5784 (p90) outliers start: 22 outliers final: 12 residues processed: 44 average time/residue: 0.8423 time to fit residues: 41.2162 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 : 0.634 ------------------------------------------------------------------------------- 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 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 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 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 27 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2183 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= 0.256 Angle : 0.609 10.406 14524 Z= 0.304 Chirality : 0.034 0.217 1810 Planarity : 0.005 0.076 923 Dihedral : 23.864 140.567 4347 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 5.10 % Allowed : 32.52 % 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: 0.23 (0.41), residues: 461 helix: 1.53 (0.31), residues: 242 sheet: -1.92 (0.58), residues: 82 loop : -0.86 (0.61), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 588 HIS 0.004 0.001 HIS A 323 PHE 0.013 0.001 PHE A 433 TYR 0.016 0.002 TYR A 590 ARG 0.003 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: 21 poor density : 23 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8445 (t0) REVERT: A 514 PHE cc_start: 0.6280 (OUTLIER) cc_final: 0.5739 (p90) outliers start: 21 outliers final: 13 residues processed: 41 average time/residue: 0.7594 time to fit residues: 35.1427 Evaluate side-chains 38 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 23 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 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 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 548 LEU 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 69 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9846 Z= 0.362 Angle : 0.681 10.090 14524 Z= 0.344 Chirality : 0.037 0.224 1810 Planarity : 0.006 0.079 923 Dihedral : 23.994 141.725 4347 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % 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: -0.22 (0.40), residues: 461 helix: 0.97 (0.31), residues: 248 sheet: -1.97 (0.61), residues: 78 loop : -0.87 (0.61), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 588 HIS 0.004 0.001 HIS A 323 PHE 0.014 0.002 PHE A 514 TYR 0.018 0.002 TYR A 590 ARG 0.005 0.001 ARG A 350 ********************** 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 44 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 24 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8443 (t0) REVERT: A 397 GLU cc_start: 0.5082 (OUTLIER) cc_final: 0.4354 (tm-30) outliers start: 20 outliers final: 13 residues processed: 42 average time/residue: 0.7319 time to fit residues: 34.8192 Evaluate side-chains 38 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 23 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 29 THR Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 66 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 23 optimal weight: 0.0980 chunk 57 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 48 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 63 optimal weight: 8.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4251 r_free = 0.4251 target = 0.113891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.090328 restraints weight = 27306.318| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.72 r_work: 0.3674 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9846 Z= 0.158 Angle : 0.575 9.424 14524 Z= 0.287 Chirality : 0.031 0.216 1810 Planarity : 0.005 0.076 923 Dihedral : 23.807 140.218 4347 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.16 % Allowed : 34.22 % 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: 0.36 (0.41), residues: 461 helix: 1.67 (0.32), residues: 242 sheet: -1.93 (0.57), residues: 82 loop : -0.83 (0.59), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 588 HIS 0.003 0.001 HIS A 342 PHE 0.011 0.001 PHE A 433 TYR 0.011 0.001 TYR A 474 ARG 0.005 0.001 ARG A 435 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2125.17 seconds wall clock time: 39 minutes 30.47 seconds (2370.47 seconds total)