Starting phenix.real_space_refine on Wed Mar 12 22:38:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n3o_24142/03_2025/7n3o_24142.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n3o_24142/03_2025/7n3o_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_24142/03_2025/7n3o_24142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n3o_24142/03_2025/7n3o_24142.map" model { file = "/net/cci-nas-00/data/ceres_data/7n3o_24142/03_2025/7n3o_24142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n3o_24142/03_2025/7n3o_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-5624/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: 5.48, per 1000 atoms: 0.66 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: 2.21 Conformation dependent library (CDL) restraints added in 465.5 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: 3.48 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: 3.49 Time building geometry restraints manager: 2.61 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: 0.560 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 25.170 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.130 ------------------------------------------------------------------------------- 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 : 0.511 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: 0.1645 time to fit residues: 19.1202 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 : 0.510 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.170444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.136787 restraints weight = 18957.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.137893 restraints weight = 12037.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.138908 restraints weight = 9499.107| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 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 : 0.565 Fit side-chains REVERT: A 349 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7594 (mt) outliers start: 6 outliers final: 3 residues processed: 72 average time/residue: 0.1625 time to fit residues: 17.4124 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 : 0.592 ------------------------------------------------------------------------------- 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 18 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.163574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.127357 restraints weight = 18860.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.129917 restraints weight = 11771.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.132496 restraints weight = 7437.890| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8922 Z= 0.295 Angle : 0.701 9.210 13152 Z= 0.351 Chirality : 0.038 0.247 1664 Planarity : 0.005 0.042 850 Dihedral : 24.262 177.052 3938 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.78 % Allowed : 17.84 % Favored : 78.38 % 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: 0.47 (0.39), residues: 446 helix: 1.42 (0.32), residues: 249 sheet: -0.74 (0.58), residues: 73 loop : -1.20 (0.51), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 324 HIS 0.005 0.001 HIS A 323 PHE 0.012 0.002 PHE A 328 TYR 0.023 0.003 TYR A 441 ARG 0.005 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: 14 poor density : 64 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.7997 (t-100) cc_final: 0.7711 (t60) REVERT: A 388 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7731 (mm-30) REVERT: A 565 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7649 (tm-30) outliers start: 14 outliers final: 7 residues processed: 70 average time/residue: 0.1791 time to fit residues: 18.1932 Evaluate side-chains 66 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 453 LEU Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 559 ILE 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 6 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 30.0000 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN A 28 ASN A 342 HIS ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.164220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.129315 restraints weight = 18559.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.131455 restraints weight = 11885.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.131398 restraints weight = 9789.932| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8922 Z= 0.212 Angle : 0.641 14.949 13152 Z= 0.320 Chirality : 0.035 0.228 1664 Planarity : 0.004 0.045 850 Dihedral : 24.155 178.328 3938 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 5.14 % Allowed : 20.54 % Favored : 74.32 % 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: 0.89 (0.39), residues: 446 helix: 1.74 (0.32), residues: 250 sheet: -0.47 (0.61), residues: 72 loop : -1.07 (0.52), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 324 HIS 0.005 0.001 HIS A 323 PHE 0.015 0.002 PHE A 328 TYR 0.020 0.002 TYR A 570 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 83 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8037 (t-100) cc_final: 0.7757 (t60) REVERT: A 388 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7522 (mm-30) REVERT: A 435 ARG cc_start: 0.7999 (mtt-85) cc_final: 0.7517 (mtt-85) REVERT: A 565 GLN cc_start: 0.8203 (tm-30) cc_final: 0.7640 (tm-30) outliers start: 19 outliers final: 10 residues processed: 77 average time/residue: 0.1832 time to fit residues: 19.9830 Evaluate side-chains 69 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 372 THR 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 564 GLU Chi-restraints excluded: chain A residue 583 VAL 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 51 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 10 optimal weight: 30.0000 chunk 16 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.149560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.113663 restraints weight = 19182.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.115759 restraints weight = 12091.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.116654 restraints weight = 8864.988| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.6963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.078 8922 Z= 0.616 Angle : 1.007 11.793 13152 Z= 0.499 Chirality : 0.052 0.254 1664 Planarity : 0.007 0.061 850 Dihedral : 24.961 176.820 3938 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 25.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 10.00 % Allowed : 18.11 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.37), residues: 446 helix: 0.33 (0.30), residues: 251 sheet: -1.00 (0.60), residues: 66 loop : -1.48 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 324 HIS 0.007 0.002 HIS A 370 PHE 0.023 0.003 PHE A 313 TYR 0.026 0.004 TYR A 91 ARG 0.008 0.001 ARG A 320 *********************** 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 95 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 58 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 435 ARG cc_start: 0.8213 (mtt-85) cc_final: 0.7593 (mtt-85) REVERT: A 565 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7818 (tm-30) REVERT: A 613 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7506 (tp-100) outliers start: 37 outliers final: 22 residues processed: 80 average time/residue: 0.1515 time to fit residues: 18.0387 Evaluate side-chains 73 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 50 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 302 CYS Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 447 ILE 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 551 MET Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 613 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 37 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.159434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.124307 restraints weight = 18760.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.125253 restraints weight = 11138.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.126311 restraints weight = 8787.794| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.6264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8922 Z= 0.168 Angle : 0.662 16.754 13152 Z= 0.330 Chirality : 0.036 0.228 1664 Planarity : 0.004 0.047 850 Dihedral : 24.534 178.814 3938 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.86 % Allowed : 25.14 % Favored : 70.00 % 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: 0.56 (0.39), residues: 446 helix: 1.42 (0.32), residues: 250 sheet: -0.58 (0.62), residues: 67 loop : -1.07 (0.53), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 382 HIS 0.004 0.001 HIS A 323 PHE 0.022 0.002 PHE A 328 TYR 0.030 0.002 TYR A 91 ARG 0.008 0.001 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 82 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8131 (t-100) cc_final: 0.7808 (t60) REVERT: A 324 TRP cc_start: 0.8194 (m100) cc_final: 0.7490 (m100) REVERT: A 435 ARG cc_start: 0.7899 (mtt-85) cc_final: 0.7549 (mtt-85) REVERT: A 438 GLN cc_start: 0.7563 (tp40) cc_final: 0.7335 (tp40) REVERT: A 565 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7525 (tm-30) outliers start: 18 outliers final: 10 residues processed: 75 average time/residue: 0.1800 time to fit residues: 19.8679 Evaluate side-chains 64 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 90 ILE 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 429 ILE Chi-restraints excluded: chain A residue 465 ASP 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 0 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 A 496 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.149165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.113239 restraints weight = 19191.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.115169 restraints weight = 11393.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.116934 restraints weight = 8055.660| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.7347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 8922 Z= 0.529 Angle : 0.918 13.481 13152 Z= 0.459 Chirality : 0.049 0.265 1664 Planarity : 0.007 0.111 850 Dihedral : 24.943 177.342 3938 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 22.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 6.22 % Allowed : 26.49 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.37), residues: 446 helix: 0.49 (0.30), residues: 250 sheet: -1.18 (0.60), residues: 68 loop : -1.35 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 324 HIS 0.006 0.002 HIS A 522 PHE 0.021 0.003 PHE A 313 TYR 0.022 0.003 TYR A 91 ARG 0.008 0.001 ARG A 320 *********************** 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 79 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8422 (t-100) cc_final: 0.8000 (t60) REVERT: A 324 TRP cc_start: 0.8456 (m100) cc_final: 0.7705 (m100) REVERT: A 435 ARG cc_start: 0.8197 (mtt-85) cc_final: 0.7542 (mtt-85) REVERT: A 565 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7503 (tm-30) outliers start: 23 outliers final: 18 residues processed: 69 average time/residue: 0.2111 time to fit residues: 21.5728 Evaluate side-chains 72 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 90 ILE 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 372 THR Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 604 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.157646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.123111 restraints weight = 19132.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.123100 restraints weight = 12139.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.125134 restraints weight = 9656.667| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.6822 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= 0.188 Angle : 0.670 15.437 13152 Z= 0.337 Chirality : 0.037 0.224 1664 Planarity : 0.004 0.043 850 Dihedral : 24.607 178.527 3938 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.05 % Allowed : 28.92 % Favored : 67.03 % 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: 0.67 (0.39), residues: 446 helix: 1.52 (0.32), residues: 250 sheet: -0.73 (0.63), residues: 67 loop : -0.96 (0.53), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 324 HIS 0.003 0.001 HIS A 500 PHE 0.022 0.002 PHE A 328 TYR 0.039 0.002 TYR A 91 ARG 0.011 0.001 ARG A 391 *********************** 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 78 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8198 (t-100) cc_final: 0.7823 (t60) REVERT: A 388 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7699 (mm-30) REVERT: A 435 ARG cc_start: 0.7847 (mtt-85) cc_final: 0.7574 (mtt-85) REVERT: A 565 GLN cc_start: 0.8151 (tm-30) cc_final: 0.7742 (tm-30) outliers start: 15 outliers final: 11 residues processed: 76 average time/residue: 0.2869 time to fit residues: 30.3166 Evaluate side-chains 70 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 90 ILE 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 429 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 604 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 55 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 30.0000 chunk 61 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS A 379 ASN A 496 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.150819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.109005 restraints weight = 19271.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.112094 restraints weight = 10061.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.113955 restraints weight = 7290.416| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.7451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 8922 Z= 0.429 Angle : 0.829 14.147 13152 Z= 0.418 Chirality : 0.045 0.254 1664 Planarity : 0.007 0.129 850 Dihedral : 24.842 178.306 3938 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.41 % Allowed : 27.57 % Favored : 67.03 % 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: -0.12 (0.38), residues: 446 helix: 0.82 (0.31), residues: 250 sheet: -1.12 (0.61), residues: 68 loop : -1.09 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 382 HIS 0.008 0.002 HIS A 370 PHE 0.017 0.002 PHE A 313 TYR 0.037 0.003 TYR A 91 ARG 0.012 0.001 ARG A 391 *********************** 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 73 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8425 (t-100) cc_final: 0.7969 (t60) REVERT: A 84 ILE cc_start: 0.5964 (OUTLIER) cc_final: 0.5740 (pt) REVERT: A 435 ARG cc_start: 0.8008 (mtt-85) cc_final: 0.7498 (mtt-85) REVERT: A 565 GLN cc_start: 0.8154 (tm-30) cc_final: 0.7463 (tm-30) outliers start: 20 outliers final: 14 residues processed: 70 average time/residue: 0.2025 time to fit residues: 22.1847 Evaluate side-chains 66 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 84 ILE Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 312 ILE 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 471 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 598 GLN 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 37 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 51 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 0 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 GLN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.151700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.109673 restraints weight = 19181.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.112875 restraints weight = 9687.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.114723 restraints weight = 6909.338| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.7451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.232 8922 Z= 0.345 Angle : 1.036 59.200 13152 Z= 0.566 Chirality : 0.045 0.359 1664 Planarity : 0.007 0.118 850 Dihedral : 24.857 178.346 3938 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.26 % Favored : 95.52 % Rotamer: Outliers : 4.32 % Allowed : 29.19 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.38), residues: 446 helix: 0.79 (0.31), residues: 250 sheet: -1.05 (0.62), residues: 68 loop : -1.20 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 382 HIS 0.005 0.002 HIS A 353 PHE 0.015 0.002 PHE A 281 TYR 0.030 0.003 TYR A 91 ARG 0.007 0.001 ARG A 616 ********************** 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 68 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8463 (t-100) cc_final: 0.7976 (t60) REVERT: A 84 ILE cc_start: 0.5919 (OUTLIER) cc_final: 0.5704 (pt) REVERT: A 435 ARG cc_start: 0.7984 (mtt-85) cc_final: 0.7482 (mtt-85) REVERT: A 565 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7485 (tm-30) outliers start: 16 outliers final: 14 residues processed: 65 average time/residue: 0.1757 time to fit residues: 17.3796 Evaluate side-chains 67 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 84 ILE Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 312 ILE 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 471 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 598 GLN 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 19 optimal weight: 0.0970 chunk 27 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 GLN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.151687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.109761 restraints weight = 19217.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.113010 restraints weight = 9702.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.114976 restraints weight = 6920.770| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.7452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.232 8922 Z= 0.345 Angle : 1.036 59.197 13152 Z= 0.566 Chirality : 0.045 0.359 1664 Planarity : 0.007 0.118 850 Dihedral : 24.857 178.346 3938 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.26 % Favored : 95.52 % Rotamer: Outliers : 4.32 % Allowed : 29.46 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.38), residues: 446 helix: 0.79 (0.31), residues: 250 sheet: -1.05 (0.62), residues: 68 loop : -1.20 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 382 HIS 0.005 0.002 HIS A 353 PHE 0.015 0.002 PHE A 281 TYR 0.030 0.003 TYR A 91 ARG 0.007 0.001 ARG A 616 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2390.27 seconds wall clock time: 45 minutes 13.44 seconds (2713.44 seconds total)