Starting phenix.real_space_refine on Tue Mar 3 19:40:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n3o_24142/03_2026/7n3o_24142.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n3o_24142/03_2026/7n3o_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 { model { file = "/net/cci-nas-00/data/ceres_data/7n3o_24142/03_2026/7n3o_24142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n3o_24142/03_2026/7n3o_24142.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n3o_24142/03_2026/7n3o_24142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n3o_24142/03_2026/7n3o_24142.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'GLU:plan': 14, 'ASP:plan': 4, 'GLN:plan1': 3, 'ARG:plan': 2} 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: 1.68, per 1000 atoms: 0.20 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: 0.60 Conformation dependent library (CDL) restraints added in 160.9 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: 1.07 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: 1.79 Time building geometry restraints manager: 0.87 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.210 Find NCS groups from input model: 0.040 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.400 ------------------------------------------------------------------------------- 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= 0.175 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.008 0.001 ARG A 17 TYR 0.016 0.002 TYR A 441 PHE 0.009 0.001 PHE A 313 TRP 0.016 0.002 TRP A 324 HIS 0.003 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8922) covalent geometry : angle 0.59407 (13152) hydrogen bonds : bond 0.11402 ( 410) hydrogen bonds : angle 4.43012 ( 1005) *********************** 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 : 0.191 Fit side-chains REVERT: A 603 GLN cc_start: 0.8122 (mt0) cc_final: 0.7730 (tt0) REVERT: A 625 GLU cc_start: 0.8290 (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: 0.0631 time to fit residues: 7.4151 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 : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.161449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.125653 restraints weight = 18937.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.128148 restraints weight = 11969.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.128945 restraints weight = 8389.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.129168 restraints weight = 6793.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.129723 restraints weight = 6344.339| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 8922 Z= 0.356 Angle : 0.879 9.955 13152 Z= 0.437 Chirality : 0.045 0.272 1664 Planarity : 0.006 0.038 850 Dihedral : 24.497 175.328 3938 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.89 % Allowed : 15.95 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.38), residues: 446 helix: 0.85 (0.31), residues: 250 sheet: -1.06 (0.58), residues: 74 loop : -1.35 (0.50), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 17 TYR 0.026 0.003 TYR A 316 PHE 0.021 0.003 PHE A 281 TRP 0.023 0.003 TRP A 324 HIS 0.010 0.003 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00730 ( 8922) covalent geometry : angle 0.87892 (13152) hydrogen bonds : bond 0.06592 ( 410) hydrogen bonds : angle 4.81013 ( 1005) *********************** 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: 7 poor density : 68 time to evaluate : 0.147 Fit side-chains REVERT: A 565 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7738 (tm-30) outliers start: 7 outliers final: 3 residues processed: 73 average time/residue: 0.0707 time to fit residues: 7.2981 Evaluate side-chains 58 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 36 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.168018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.132503 restraints weight = 18257.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.135599 restraints weight = 11112.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.136201 restraints weight = 7779.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.136466 restraints weight = 6503.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.136793 restraints weight = 6059.789| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.3925 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= 0.127 Angle : 0.615 9.976 13152 Z= 0.308 Chirality : 0.034 0.237 1664 Planarity : 0.004 0.042 850 Dihedral : 24.153 175.818 3938 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.43 % Allowed : 19.46 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.39), residues: 446 helix: 1.63 (0.32), residues: 249 sheet: -0.62 (0.58), residues: 75 loop : -1.16 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 391 TYR 0.019 0.002 TYR A 590 PHE 0.018 0.002 PHE A 328 TRP 0.013 0.001 TRP A 324 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8922) covalent geometry : angle 0.61491 (13152) hydrogen bonds : bond 0.04203 ( 410) hydrogen bonds : angle 3.93210 ( 1005) *********************** 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 74 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5358 (ppp) cc_final: 0.5040 (ppp) REVERT: A 21 TRP cc_start: 0.7984 (t-100) cc_final: 0.7728 (t60) outliers start: 9 outliers final: 5 residues processed: 70 average time/residue: 0.0653 time to fit residues: 6.8951 Evaluate side-chains 62 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 465 ASP 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 25 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 342 HIS A 379 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.153882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.118286 restraints weight = 19439.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.120895 restraints weight = 12075.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.121338 restraints weight = 8687.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.121703 restraints weight = 6927.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.122239 restraints weight = 6371.108| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.6124 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= 0.371 Angle : 0.913 13.682 13152 Z= 0.454 Chirality : 0.047 0.269 1664 Planarity : 0.006 0.045 850 Dihedral : 24.660 177.228 3938 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 22.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 7.03 % Allowed : 20.81 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.38), residues: 446 helix: 0.75 (0.31), residues: 250 sheet: -0.68 (0.61), residues: 61 loop : -1.48 (0.50), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 17 TYR 0.021 0.003 TYR A 91 PHE 0.021 0.003 PHE A 313 TRP 0.017 0.002 TRP A 324 HIS 0.006 0.001 HIS A 522 Details of bonding type rmsd covalent geometry : bond 0.00756 ( 8922) covalent geometry : angle 0.91332 (13152) hydrogen bonds : bond 0.06951 ( 410) hydrogen bonds : angle 5.00898 ( 1005) *********************** 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 84 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8300 (t-100) cc_final: 0.7934 (t60) REVERT: A 565 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7552 (tm-30) REVERT: A 613 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7345 (tp-100) outliers start: 26 outliers final: 11 residues processed: 76 average time/residue: 0.0640 time to fit residues: 7.3736 Evaluate side-chains 66 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 379 ASN 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 34 optimal weight: 0.5980 chunk 24 optimal weight: 30.0000 chunk 5 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 overall best weight: 4.4586 ------------------------------------------------------------------------------- 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 489 ASN A 496 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.152645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.117047 restraints weight = 19051.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.118195 restraints weight = 11385.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.119487 restraints weight = 8877.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.119681 restraints weight = 7056.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.120050 restraints weight = 6480.326| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.6700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 8922 Z= 0.326 Angle : 0.809 13.920 13152 Z= 0.409 Chirality : 0.044 0.262 1664 Planarity : 0.006 0.046 850 Dihedral : 24.772 179.295 3938 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 8.92 % Allowed : 21.62 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.37), residues: 446 helix: 0.66 (0.31), residues: 248 sheet: -0.80 (0.63), residues: 61 loop : -1.44 (0.48), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 391 TYR 0.025 0.003 TYR A 91 PHE 0.017 0.002 PHE A 313 TRP 0.014 0.002 TRP A 382 HIS 0.005 0.002 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00666 ( 8922) covalent geometry : angle 0.80949 (13152) hydrogen bonds : bond 0.06056 ( 410) hydrogen bonds : angle 4.77871 ( 1005) *********************** 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 90 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 57 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8311 (t-100) cc_final: 0.8046 (t60) REVERT: A 388 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7646 (mp0) REVERT: A 565 GLN cc_start: 0.8125 (tm-30) cc_final: 0.7717 (tm-30) outliers start: 33 outliers final: 22 residues processed: 79 average time/residue: 0.0581 time to fit residues: 7.1003 Evaluate side-chains 73 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 51 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 64 GLN 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 308 LEU 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 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 487 LEU Chi-restraints excluded: chain A residue 489 ASN Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 564 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 32 optimal weight: 5.9990 chunk 23 optimal weight: 30.0000 chunk 44 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 HIS A 489 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 = 0.4101 r_free = 0.4101 target = 0.151303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.110802 restraints weight = 18760.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.113930 restraints weight = 9701.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.115680 restraints weight = 6933.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.116737 restraints weight = 5931.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.116737 restraints weight = 5485.699| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.7291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 8922 Z= 0.358 Angle : 0.860 14.336 13152 Z= 0.434 Chirality : 0.046 0.257 1664 Planarity : 0.006 0.074 850 Dihedral : 24.883 178.620 3938 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 9.46 % Allowed : 23.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.37), residues: 446 helix: 0.40 (0.31), residues: 250 sheet: -1.03 (0.65), residues: 61 loop : -1.49 (0.49), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 17 TYR 0.027 0.003 TYR A 91 PHE 0.019 0.003 PHE A 313 TRP 0.014 0.002 TRP A 324 HIS 0.005 0.002 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00735 ( 8922) covalent geometry : angle 0.85957 (13152) hydrogen bonds : bond 0.06667 ( 410) hydrogen bonds : angle 4.95055 ( 1005) *********************** 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 87 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 52 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8383 (t-100) cc_final: 0.8073 (t60) REVERT: A 84 ILE cc_start: 0.6051 (OUTLIER) cc_final: 0.5803 (pt) REVERT: A 565 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7305 (tm-30) REVERT: A 613 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7551 (tp-100) outliers start: 35 outliers final: 22 residues processed: 75 average time/residue: 0.0544 time to fit residues: 6.4890 Evaluate side-chains 73 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 49 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 84 ILE 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 372 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 377 VAL 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 496 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.0010 overall best weight: 0.9190 ------------------------------------------------------------------------------- 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 = 0.4203 r_free = 0.4203 target = 0.158228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.117514 restraints weight = 19076.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.120923 restraints weight = 9407.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.123073 restraints weight = 6567.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.124158 restraints weight = 5513.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.124469 restraints weight = 5086.863| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.6704 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= 0.134 Angle : 0.668 17.466 13152 Z= 0.333 Chirality : 0.036 0.226 1664 Planarity : 0.004 0.047 850 Dihedral : 24.537 178.350 3938 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.95 % Allowed : 27.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.39), residues: 446 helix: 1.18 (0.32), residues: 250 sheet: -0.50 (0.63), residues: 60 loop : -1.01 (0.52), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 391 TYR 0.010 0.002 TYR A 570 PHE 0.024 0.002 PHE A 328 TRP 0.020 0.002 TRP A 324 HIS 0.007 0.002 HIS A 369 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8922) covalent geometry : angle 0.66831 (13152) hydrogen bonds : bond 0.04491 ( 410) hydrogen bonds : angle 4.18757 ( 1005) *********************** 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 81 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8238 (t-100) cc_final: 0.7865 (t60) REVERT: A 34 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8224 (tm-30) REVERT: A 388 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7595 (mp0) REVERT: A 452 SER cc_start: 0.7624 (t) cc_final: 0.7356 (p) REVERT: A 625 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7802 (tm-30) outliers start: 22 outliers final: 12 residues processed: 73 average time/residue: 0.0587 time to fit residues: 6.5853 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 : 0.184 ------------------------------------------------------------------------------- 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 34 GLU Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 90 ILE 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 379 ASN Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 564 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 13 optimal weight: 0.0980 chunk 6 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.151821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.117085 restraints weight = 18640.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.118576 restraints weight = 12771.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.119712 restraints weight = 8211.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.120077 restraints weight = 7065.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.120540 restraints weight = 6807.145| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.7405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 8922 Z= 0.345 Angle : 0.844 15.060 13152 Z= 0.425 Chirality : 0.045 0.252 1664 Planarity : 0.005 0.045 850 Dihedral : 24.769 178.217 3938 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.41 % Allowed : 28.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.38), residues: 446 helix: 0.59 (0.31), residues: 250 sheet: -0.96 (0.61), residues: 68 loop : -1.22 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 380 TYR 0.018 0.002 TYR A 538 PHE 0.020 0.003 PHE A 313 TRP 0.016 0.002 TRP A 324 HIS 0.010 0.002 HIS A 369 Details of bonding type rmsd covalent geometry : bond 0.00705 ( 8922) covalent geometry : angle 0.84356 (13152) hydrogen bonds : bond 0.06188 ( 410) hydrogen bonds : angle 4.78575 ( 1005) *********************** 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: 20 poor density : 56 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8242 (t-100) cc_final: 0.7918 (t60) REVERT: A 282 PRO cc_start: 0.8543 (Cg_exo) cc_final: 0.8335 (Cg_endo) REVERT: A 625 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8120 (tm-30) outliers start: 20 outliers final: 15 residues processed: 73 average time/residue: 0.0544 time to fit residues: 6.2870 Evaluate side-chains 68 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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 377 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 28 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN A 496 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.159421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.118914 restraints weight = 18817.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.122340 restraints weight = 9344.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.124498 restraints weight = 6495.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.125231 restraints weight = 5459.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.125314 restraints weight = 5097.650| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.6867 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= 0.130 Angle : 0.658 16.437 13152 Z= 0.332 Chirality : 0.035 0.222 1664 Planarity : 0.004 0.041 850 Dihedral : 24.459 177.992 3938 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.59 % Allowed : 30.27 % Favored : 65.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.39), residues: 446 helix: 1.44 (0.32), residues: 250 sheet: -0.49 (0.62), residues: 67 loop : -1.12 (0.53), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 391 TYR 0.017 0.002 TYR A 497 PHE 0.023 0.002 PHE A 328 TRP 0.018 0.002 TRP A 324 HIS 0.006 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8922) covalent geometry : angle 0.65847 (13152) hydrogen bonds : bond 0.04149 ( 410) hydrogen bonds : angle 4.02790 ( 1005) *********************** 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 75 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8095 (t-100) cc_final: 0.7748 (t60) REVERT: A 289 GLU cc_start: 0.7528 (mp0) cc_final: 0.7303 (mp0) REVERT: A 452 SER cc_start: 0.7587 (t) cc_final: 0.7363 (p) REVERT: A 489 ASN cc_start: 0.8205 (OUTLIER) cc_final: 0.7735 (t0) REVERT: A 498 LEU cc_start: 0.7973 (tt) cc_final: 0.7681 (tp) REVERT: A 551 MET cc_start: 0.6417 (ppp) cc_final: 0.6067 (ppp) REVERT: A 625 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7797 (tm-30) outliers start: 17 outliers final: 11 residues processed: 72 average time/residue: 0.0655 time to fit residues: 7.3597 Evaluate side-chains 69 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 377 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 489 ASN Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 583 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 55 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 36 optimal weight: 0.0570 chunk 22 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN A 489 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 = 0.4196 r_free = 0.4196 target = 0.157768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.123252 restraints weight = 18690.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.122625 restraints weight = 11474.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.124889 restraints weight = 9825.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.124708 restraints weight = 7086.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.125301 restraints weight = 6842.400| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.6840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8922 Z= 0.150 Angle : 0.660 16.768 13152 Z= 0.330 Chirality : 0.035 0.227 1664 Planarity : 0.004 0.042 850 Dihedral : 24.343 178.693 3938 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.78 % Allowed : 30.54 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.39), residues: 446 helix: 1.50 (0.32), residues: 250 sheet: -0.58 (0.63), residues: 65 loop : -0.98 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 391 TYR 0.011 0.002 TYR A 570 PHE 0.017 0.002 PHE A 328 TRP 0.018 0.001 TRP A 324 HIS 0.005 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8922) covalent geometry : angle 0.65999 (13152) hydrogen bonds : bond 0.04354 ( 410) hydrogen bonds : angle 4.07560 ( 1005) ********************** 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 71 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 MET cc_start: 0.3156 (mmm) cc_final: 0.1779 (mmp) REVERT: A 452 SER cc_start: 0.7515 (t) cc_final: 0.7304 (p) REVERT: A 625 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7827 (tm-30) outliers start: 14 outliers final: 13 residues processed: 68 average time/residue: 0.0650 time to fit residues: 6.9321 Evaluate side-chains 69 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 379 ASN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 471 VAL 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 43 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 4 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.157311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.122445 restraints weight = 18865.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.123079 restraints weight = 11825.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.124419 restraints weight = 9286.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.124667 restraints weight = 7348.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.124895 restraints weight = 7255.262| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.6875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.169 8922 Z= 0.283 Angle : 1.072 59.200 13152 Z= 0.646 Chirality : 0.038 0.305 1664 Planarity : 0.008 0.162 850 Dihedral : 24.343 178.674 3938 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.59 % Allowed : 29.46 % Favored : 65.95 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.39), residues: 446 helix: 1.39 (0.32), residues: 250 sheet: -0.56 (0.63), residues: 65 loop : -1.10 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 391 TYR 0.014 0.002 TYR A 570 PHE 0.014 0.002 PHE A 328 TRP 0.083 0.009 TRP A 324 HIS 0.020 0.002 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00574 ( 8922) covalent geometry : angle 1.07171 (13152) hydrogen bonds : bond 0.04465 ( 410) hydrogen bonds : angle 4.08805 ( 1005) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1207.40 seconds wall clock time: 21 minutes 38.63 seconds (1298.63 seconds total)