Starting phenix.real_space_refine on Sat Dec 28 11:01:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n3o_24142/12_2024/7n3o_24142.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n3o_24142/12_2024/7n3o_24142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n3o_24142/12_2024/7n3o_24142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n3o_24142/12_2024/7n3o_24142.map" model { file = "/net/cci-nas-00/data/ceres_data/7n3o_24142/12_2024/7n3o_24142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n3o_24142/12_2024/7n3o_24142.cif" } resolution = 3.8 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= 0.002 sd= 0.084 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 222 5.49 5 S 12 5.16 5 C 4378 2.51 5 N 1500 2.21 5 O 2183 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 8295 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3561 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 16, 'TRANS': 437} Chain breaks: 3 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 14, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "B" Number of atoms: 4734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 4734 Classifications: {'RNA': 222} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 15, 'rna3p_pur': 99, 'rna3p_pyr': 91} Link IDs: {'rna2p': 32, 'rna3p': 189} Chain breaks: 4 Time building chain proxies: 5.25, per 1000 atoms: 0.63 Number of scatterers: 8295 At special positions: 0 Unit cell: (97.65, 105, 118.65, 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 12 16.00 P 222 15.00 O 2183 8.00 N 1500 7.00 C 4378 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: 2.23 Conformation dependent library (CDL) restraints added in 473.9 milliseconds 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 858 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 59.5% alpha, 11.0% beta 71 base pairs and 121 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain 'A' and resid 13 through 25 Processing helix chain 'A' and resid 27 through 42 Processing helix chain 'A' and resid 44 through 51 removed outlier: 4.113A pdb=" N GLN A 50 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS A 51 " --> pdb=" O LYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 64 removed outlier: 4.076A pdb=" N VAL A 59 " --> pdb=" O PRO A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.506A pdb=" N THR A 68 " --> pdb=" O PRO A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 102 Processing helix chain 'A' and resid 318 through 338 removed outlier: 4.455A pdb=" N HIS A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N TRP A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 379 through 382 Processing helix chain 'A' and resid 383 through 406 Processing helix chain 'A' and resid 413 through 430 removed outlier: 3.632A pdb=" N ASN A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 removed outlier: 3.535A pdb=" N LEU A 481 " --> pdb=" O ILE A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 505 removed outlier: 3.860A pdb=" N ASN A 489 " --> pdb=" O TYR A 485 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 538 removed outlier: 3.846A pdb=" N HIS A 522 " --> pdb=" O GLU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 567 Processing helix chain 'A' and resid 570 through 585 Processing helix chain 'A' and resid 589 through 605 Processing helix chain 'A' and resid 618 through 637 Processing sheet with id=AA1, first strand: chain 'A' and resid 283 through 284 removed outlier: 3.648A pdb=" N ASN A 351 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU A 371 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU A 301 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 471 through 475 removed outlier: 3.625A pdb=" N GLY A 611 " --> pdb=" O LEU A 545 " (cutoff:3.500A) 229 hydrogen bonds defined for protein. 663 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 181 hydrogen bonds 342 hydrogen bond angles 0 basepair planarities 71 basepair parallelities 121 stacking parallelities Total time for adding SS restraints: 3.57 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1019 1.33 - 1.45: 3605 1.45 - 1.57: 3841 1.57 - 1.69: 439 1.69 - 1.81: 18 Bond restraints: 8922 Sorted by residual: bond pdb=" N LEU A 308 " pdb=" CA LEU A 308 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.06e+00 bond pdb=" N THR A 387 " pdb=" CA THR A 387 " ideal model delta sigma weight residual 1.459 1.492 -0.034 1.28e-02 6.10e+03 6.94e+00 bond pdb=" O3' G B 56 " pdb=" P G B 57 " ideal model delta sigma weight residual 1.607 1.646 -0.039 1.50e-02 4.44e+03 6.68e+00 bond pdb=" C PRO A 280 " pdb=" O PRO A 280 " ideal model delta sigma weight residual 1.234 1.204 0.029 1.14e-02 7.69e+03 6.67e+00 bond pdb=" N VAL A 284 " pdb=" CA VAL A 284 " ideal model delta sigma weight residual 1.449 1.494 -0.046 1.80e-02 3.09e+03 6.43e+00 ... (remaining 8917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 12772 1.54 - 3.07: 288 3.07 - 4.61: 66 4.61 - 6.14: 21 6.14 - 7.68: 5 Bond angle restraints: 13152 Sorted by residual: angle pdb=" CA VAL A 284 " pdb=" C VAL A 284 " pdb=" O VAL A 284 " ideal model delta sigma weight residual 121.68 117.41 4.27 7.90e-01 1.60e+00 2.92e+01 angle pdb=" O3' G B 56 " pdb=" C3' G B 56 " pdb=" C2' G B 56 " ideal model delta sigma weight residual 109.50 116.75 -7.25 1.50e+00 4.44e-01 2.34e+01 angle pdb=" CA PHE A 285 " pdb=" C PHE A 285 " pdb=" N GLU A 286 " ideal model delta sigma weight residual 115.81 121.14 -5.33 1.15e+00 7.56e-01 2.15e+01 angle pdb=" CA PHE A 285 " pdb=" CB PHE A 285 " pdb=" CG PHE A 285 " ideal model delta sigma weight residual 113.80 117.63 -3.83 1.00e+00 1.00e+00 1.47e+01 angle pdb=" CA PHE A 285 " pdb=" C PHE A 285 " pdb=" O PHE A 285 " ideal model delta sigma weight residual 120.63 116.66 3.97 1.05e+00 9.07e-01 1.43e+01 ... (remaining 13147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 4996 35.84 - 71.67: 558 71.67 - 107.51: 66 107.51 - 143.34: 4 143.34 - 179.18: 8 Dihedral angle restraints: 5632 sinusoidal: 4309 harmonic: 1323 Sorted by residual: dihedral pdb=" O4' C B 196 " pdb=" C1' C B 196 " pdb=" N1 C B 196 " pdb=" C2 C B 196 " ideal model delta sinusoidal sigma weight residual 200.00 24.17 175.83 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U B 60 " pdb=" C1' U B 60 " pdb=" N1 U B 60 " pdb=" C2 U B 60 " ideal model delta sinusoidal sigma weight residual 232.00 52.82 179.18 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 98 " pdb=" C1' U B 98 " pdb=" N1 U B 98 " pdb=" C2 U B 98 " ideal model delta sinusoidal sigma weight residual 232.00 64.46 167.54 1 1.70e+01 3.46e-03 6.57e+01 ... (remaining 5629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1557 0.068 - 0.135: 81 0.135 - 0.203: 18 0.203 - 0.270: 5 0.270 - 0.338: 3 Chirality restraints: 1664 Sorted by residual: chirality pdb=" C3' G B 56 " pdb=" C4' G B 56 " pdb=" O3' G B 56 " pdb=" C2' G B 56 " both_signs ideal model delta sigma weight residual False -2.74 -2.41 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" P G B 57 " pdb=" OP1 G B 57 " pdb=" OP2 G B 57 " pdb=" O5' G B 57 " both_signs ideal model delta sigma weight residual True 2.41 -2.73 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" P G B 56 " pdb=" OP1 G B 56 " pdb=" OP2 G B 56 " pdb=" O5' G B 56 " both_signs ideal model delta sigma weight residual True 2.41 -2.73 -0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 1661 not shown) Planarity restraints: 850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 281 " 0.014 2.00e-02 2.50e+03 2.67e-02 7.11e+00 pdb=" C PHE A 281 " -0.046 2.00e-02 2.50e+03 pdb=" O PHE A 281 " 0.017 2.00e-02 2.50e+03 pdb=" N PRO A 282 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 45 " 0.031 2.00e-02 2.50e+03 1.52e-02 5.17e+00 pdb=" N1 U B 45 " -0.027 2.00e-02 2.50e+03 pdb=" C2 U B 45 " -0.009 2.00e-02 2.50e+03 pdb=" O2 U B 45 " -0.004 2.00e-02 2.50e+03 pdb=" N3 U B 45 " 0.007 2.00e-02 2.50e+03 pdb=" C4 U B 45 " 0.003 2.00e-02 2.50e+03 pdb=" O4 U B 45 " 0.008 2.00e-02 2.50e+03 pdb=" C5 U B 45 " 0.003 2.00e-02 2.50e+03 pdb=" C6 U B 45 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 613 " -0.033 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO A 614 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 614 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 614 " -0.027 5.00e-02 4.00e+02 ... (remaining 847 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2008 2.81 - 3.33: 7404 3.33 - 3.85: 16020 3.85 - 4.38: 18102 4.38 - 4.90: 25371 Nonbonded interactions: 68905 Sorted by model distance: nonbonded pdb=" O2' U B 89 " pdb=" OP1 U B 90 " model vdw 2.285 3.040 nonbonded pdb=" O ALA A 25 " pdb=" OG1 THR A 29 " model vdw 2.286 3.040 nonbonded pdb=" O2 C B 28 " pdb=" N2 G B 31 " model vdw 2.301 3.120 nonbonded pdb=" O PHE A 72 " pdb=" OH TYR A 80 " model vdw 2.311 3.040 nonbonded pdb=" NE2 GLN A 560 " pdb=" OE2 GLU A 564 " model vdw 2.315 3.120 ... (remaining 68900 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.840 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 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 0.046 8922 Z= 0.182 Angle : 0.594 7.679 13152 Z= 0.336 Chirality : 0.038 0.338 1664 Planarity : 0.004 0.049 850 Dihedral : 23.642 179.181 4774 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.35 % Allowed : 0.54 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.39), residues: 446 helix: 2.17 (0.33), residues: 239 sheet: -0.31 (0.61), residues: 75 loop : -1.39 (0.46), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 324 HIS 0.003 0.001 HIS A 42 PHE 0.009 0.001 PHE A 313 TYR 0.016 0.002 TYR A 441 ARG 0.008 0.001 ARG A 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.536 Fit side-chains REVERT: A 603 GLN cc_start: 0.8122 (mt0) cc_final: 0.7730 (tt0) REVERT: A 625 GLU cc_start: 0.8291 (tm-30) cc_final: 0.8032 (tm-30) REVERT: A 626 LEU cc_start: 0.8058 (tp) cc_final: 0.7827 (tp) outliers start: 5 outliers final: 0 residues processed: 79 average time/residue: 0.1671 time to fit residues: 19.3330 Evaluate side-chains 58 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS A 333 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8922 Z= 0.284 Angle : 0.692 9.342 13152 Z= 0.347 Chirality : 0.037 0.240 1664 Planarity : 0.005 0.044 850 Dihedral : 24.218 174.339 3938 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.62 % Allowed : 12.70 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.39), residues: 446 helix: 1.60 (0.32), residues: 249 sheet: -0.63 (0.61), residues: 74 loop : -1.12 (0.51), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 324 HIS 0.006 0.002 HIS A 370 PHE 0.016 0.002 PHE A 281 TYR 0.017 0.002 TYR A 474 ARG 0.012 0.001 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.558 Fit side-chains REVERT: A 349 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7624 (mt) outliers start: 6 outliers final: 3 residues processed: 72 average time/residue: 0.1703 time to fit residues: 18.3163 Evaluate side-chains 59 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 559 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 60 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 342 HIS A 370 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 8922 Z= 0.408 Angle : 0.844 11.250 13152 Z= 0.420 Chirality : 0.045 0.253 1664 Planarity : 0.006 0.042 850 Dihedral : 24.571 179.929 3938 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.32 % Allowed : 18.92 % Favored : 76.76 % 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 (0.38), residues: 446 helix: 0.97 (0.32), residues: 250 sheet: -0.52 (0.61), residues: 66 loop : -1.50 (0.50), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 293 HIS 0.006 0.002 HIS A 370 PHE 0.013 0.003 PHE A 313 TYR 0.022 0.004 TYR A 441 ARG 0.008 0.001 ARG A 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8113 (t-100) cc_final: 0.7736 (t60) REVERT: A 324 TRP cc_start: 0.8227 (m100) cc_final: 0.7442 (m100) REVERT: A 388 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8075 (mm-30) REVERT: A 565 GLN cc_start: 0.8189 (tm-30) cc_final: 0.7668 (tm-30) outliers start: 16 outliers final: 8 residues processed: 70 average time/residue: 0.1964 time to fit residues: 19.3991 Evaluate side-chains 65 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 598 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN A 342 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8922 Z= 0.246 Angle : 0.671 14.801 13152 Z= 0.337 Chirality : 0.037 0.232 1664 Planarity : 0.004 0.048 850 Dihedral : 24.350 179.190 3938 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.68 % Allowed : 21.35 % Favored : 72.97 % 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: 0.55 (0.39), residues: 446 helix: 1.47 (0.32), residues: 250 sheet: -0.82 (0.60), residues: 70 loop : -1.10 (0.52), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 324 HIS 0.003 0.001 HIS A 323 PHE 0.016 0.002 PHE A 328 TYR 0.019 0.002 TYR A 441 ARG 0.006 0.001 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8099 (t-100) cc_final: 0.7759 (t60) REVERT: A 324 TRP cc_start: 0.8210 (m100) cc_final: 0.7546 (m100) REVERT: A 435 ARG cc_start: 0.7916 (mtt-85) cc_final: 0.7433 (mtt-85) REVERT: A 565 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7594 (tm-30) outliers start: 21 outliers final: 10 residues processed: 80 average time/residue: 0.1620 time to fit residues: 19.1710 Evaluate side-chains 71 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 598 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 0.0040 chunk 12 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN A 496 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.6222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8922 Z= 0.314 Angle : 0.727 14.790 13152 Z= 0.365 Chirality : 0.040 0.238 1664 Planarity : 0.005 0.046 850 Dihedral : 24.498 178.728 3938 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 7.57 % Allowed : 21.35 % Favored : 71.08 % 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 (0.38), residues: 446 helix: 1.12 (0.32), residues: 250 sheet: -0.53 (0.62), residues: 65 loop : -1.26 (0.50), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 324 HIS 0.004 0.001 HIS A 586 PHE 0.015 0.002 PHE A 313 TYR 0.024 0.002 TYR A 91 ARG 0.004 0.001 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 63 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8188 (t-100) cc_final: 0.7903 (t60) REVERT: A 435 ARG cc_start: 0.7985 (mtt-85) cc_final: 0.7716 (mtt-85) REVERT: A 565 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7554 (tm-30) outliers start: 28 outliers final: 17 residues processed: 79 average time/residue: 0.1649 time to fit residues: 19.1990 Evaluate side-chains 77 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 598 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 7 optimal weight: 0.0970 chunk 36 optimal weight: 0.5980 chunk 47 optimal weight: 10.0000 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8922 Z= 0.143 Angle : 0.628 16.561 13152 Z= 0.312 Chirality : 0.034 0.215 1664 Planarity : 0.004 0.046 850 Dihedral : 24.272 178.568 3938 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 5.68 % Allowed : 24.59 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.40), residues: 446 helix: 1.81 (0.32), residues: 250 sheet: -0.54 (0.60), residues: 72 loop : -0.95 (0.53), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 382 HIS 0.003 0.001 HIS A 500 PHE 0.019 0.001 PHE A 328 TYR 0.013 0.001 TYR A 441 ARG 0.004 0.000 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7633 (mtm-85) cc_final: 0.7348 (mtm-85) REVERT: A 21 TRP cc_start: 0.7987 (t-100) cc_final: 0.7781 (t60) REVERT: A 280 PRO cc_start: 0.8410 (Cg_exo) cc_final: 0.8001 (Cg_endo) REVERT: A 388 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7485 (mm-30) REVERT: A 435 ARG cc_start: 0.7701 (mtt-85) cc_final: 0.7389 (mtt-85) REVERT: A 452 SER cc_start: 0.7433 (t) cc_final: 0.7201 (p) REVERT: A 453 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7860 (mm) REVERT: A 498 LEU cc_start: 0.8121 (tt) cc_final: 0.7906 (tp) REVERT: A 565 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7471 (tm-30) outliers start: 21 outliers final: 13 residues processed: 78 average time/residue: 0.1807 time to fit residues: 20.1415 Evaluate side-chains 78 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 583 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 29 optimal weight: 0.0050 chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 0.0770 chunk 12 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.4952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 HIS A 379 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8922 Z= 0.131 Angle : 0.588 16.332 13152 Z= 0.290 Chirality : 0.032 0.219 1664 Planarity : 0.004 0.038 850 Dihedral : 24.049 178.459 3938 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 5.41 % Allowed : 24.05 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.39), residues: 446 helix: 2.08 (0.32), residues: 250 sheet: -0.07 (0.64), residues: 65 loop : -0.93 (0.50), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 588 HIS 0.005 0.001 HIS A 342 PHE 0.015 0.001 PHE A 328 TYR 0.028 0.002 TYR A 570 ARG 0.009 0.000 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 MET cc_start: 0.2288 (mmm) cc_final: 0.1641 (mmp) REVERT: A 435 ARG cc_start: 0.7553 (mtt-85) cc_final: 0.7276 (mtt-85) REVERT: A 565 GLN cc_start: 0.8095 (tm-30) cc_final: 0.7514 (tm-30) REVERT: A 625 GLU cc_start: 0.8372 (tm-30) cc_final: 0.7888 (tm-30) REVERT: A 626 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7948 (tp) outliers start: 20 outliers final: 15 residues processed: 76 average time/residue: 0.1859 time to fit residues: 20.4145 Evaluate side-chains 73 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 626 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 HIS A 379 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8922 Z= 0.285 Angle : 0.688 12.452 13152 Z= 0.348 Chirality : 0.038 0.241 1664 Planarity : 0.005 0.059 850 Dihedral : 24.299 179.833 3938 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.59 % Allowed : 26.76 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.38), residues: 446 helix: 1.28 (0.31), residues: 250 sheet: -0.31 (0.63), residues: 65 loop : -0.88 (0.50), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 21 HIS 0.004 0.001 HIS A 323 PHE 0.013 0.002 PHE A 313 TYR 0.023 0.002 TYR A 570 ARG 0.013 0.001 ARG A 17 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 ARG cc_start: 0.7932 (mtt-85) cc_final: 0.7459 (mtt-85) REVERT: A 551 MET cc_start: 0.6319 (ppp) cc_final: 0.6002 (ppp) REVERT: A 565 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7561 (tm-30) REVERT: A 626 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8156 (tp) outliers start: 17 outliers final: 13 residues processed: 72 average time/residue: 0.1941 time to fit residues: 19.9142 Evaluate side-chains 70 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 626 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.6917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8922 Z= 0.344 Angle : 0.745 12.665 13152 Z= 0.380 Chirality : 0.041 0.237 1664 Planarity : 0.006 0.091 850 Dihedral : 24.566 178.882 3938 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 5.14 % Allowed : 26.76 % Favored : 68.11 % 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: 0.32 (0.38), residues: 446 helix: 1.07 (0.32), residues: 250 sheet: -0.35 (0.64), residues: 65 loop : -1.04 (0.50), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 21 HIS 0.005 0.001 HIS A 586 PHE 0.016 0.002 PHE A 313 TYR 0.024 0.003 TYR A 570 ARG 0.015 0.001 ARG A 17 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 ARG cc_start: 0.7890 (mtt-85) cc_final: 0.7547 (mtt-85) REVERT: A 452 SER cc_start: 0.7789 (t) cc_final: 0.7548 (p) REVERT: A 551 MET cc_start: 0.6692 (ppp) cc_final: 0.6359 (ppp) REVERT: A 565 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7788 (tm-30) outliers start: 19 outliers final: 14 residues processed: 73 average time/residue: 0.1701 time to fit residues: 18.2936 Evaluate side-chains 71 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 604 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN A 489 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.6576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8922 Z= 0.175 Angle : 0.644 14.643 13152 Z= 0.324 Chirality : 0.034 0.225 1664 Planarity : 0.005 0.075 850 Dihedral : 24.292 178.382 3938 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.51 % Allowed : 28.92 % Favored : 67.57 % 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: 0.92 (0.40), residues: 446 helix: 1.52 (0.32), residues: 249 sheet: -0.13 (0.64), residues: 67 loop : -0.67 (0.53), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 21 HIS 0.003 0.001 HIS A 500 PHE 0.017 0.002 PHE A 328 TYR 0.026 0.002 TYR A 570 ARG 0.008 0.001 ARG A 391 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7877 (tt0) REVERT: A 435 ARG cc_start: 0.7713 (mtt-85) cc_final: 0.7430 (mtt-85) REVERT: A 453 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7917 (mm) REVERT: A 551 MET cc_start: 0.6370 (ppp) cc_final: 0.6034 (ppp) REVERT: A 565 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7686 (tm-30) REVERT: A 625 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7905 (tm-30) outliers start: 13 outliers final: 12 residues processed: 71 average time/residue: 0.1923 time to fit residues: 19.4964 Evaluate side-chains 68 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 489 ASN Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 604 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.152923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.116921 restraints weight = 18862.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.118465 restraints weight = 12892.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.121280 restraints weight = 8626.517| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.7238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 8922 Z= 0.419 Angle : 0.827 12.116 13152 Z= 0.420 Chirality : 0.044 0.249 1664 Planarity : 0.006 0.052 850 Dihedral : 24.587 179.384 3938 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.51 % Allowed : 27.30 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.38), residues: 446 helix: 0.66 (0.31), residues: 250 sheet: -0.53 (0.63), residues: 65 loop : -0.87 (0.51), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP A 21 HIS 0.005 0.002 HIS A 522 PHE 0.019 0.002 PHE A 313 TYR 0.026 0.003 TYR A 570 ARG 0.013 0.001 ARG A 391 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1350.98 seconds wall clock time: 25 minutes 51.69 seconds (1551.69 seconds total)