Starting phenix.real_space_refine on Fri Sep 11 07:07:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7n3o_24142/09_2026/7n3o_24142.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n3o_24142/09_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_24142/09_2026/7n3o_24142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n3o_24142/09_2026/7n3o_24142.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7n3o_24142/09_2026/7n3o_24142.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7n3o_24142/09_2026/7n3o_24142.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n3o_24142/09_2026/7n3o_24142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n3o_24142/09_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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: 1.83, per 1000 atoms: 0.22 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: 0.76 Conformation dependent library (CDL) restraints added in 151.5 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: 1.18 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: 1.89 Time building geometry restraints manager: 1.02 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=" O3' G B 56 " pdb=" P G B 57 " ideal model delta sigma weight residual 1.607 1.646 -0.039 1.20e-02 6.94e+03 1.04e+01 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=" 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: 12137 1.54 - 3.07: 793 3.07 - 4.61: 163 4.61 - 6.14: 54 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=" 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 angle pdb=" C3' U B 89 " pdb=" O3' U B 89 " pdb=" P U B 90 " ideal model delta sigma weight residual 119.70 124.23 -4.53 1.20e+00 6.94e-01 1.43e+01 ... (remaining 13147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.24: 4318 33.24 - 66.48: 469 66.48 - 99.71: 43 99.71 - 132.95: 1 132.95 - 166.19: 5 Dihedral angle restraints: 4836 sinusoidal: 3513 harmonic: 1323 Sorted by residual: dihedral pdb=" C4' A B 22 " pdb=" C3' A B 22 " pdb=" C2' A B 22 " pdb=" C1' A B 22 " ideal model delta sinusoidal sigma weight residual 36.34 -37.54 73.89 1 3.10e+00 1.04e-01 7.22e+02 dihedral pdb=" C4' G B 189 " pdb=" C3' G B 189 " pdb=" C2' G B 189 " pdb=" C1' G B 189 " ideal model delta sinusoidal sigma weight residual 36.34 -37.28 73.62 1 3.10e+00 1.04e-01 7.17e+02 dihedral pdb=" C4' G B 31 " pdb=" C3' G B 31 " pdb=" C2' G B 31 " pdb=" C1' G B 31 " ideal model delta sinusoidal sigma weight residual 36.34 -36.10 72.44 1 3.10e+00 1.04e-01 6.98e+02 ... (remaining 4833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1341 0.112 - 0.223: 41 0.223 - 0.335: 279 0.335 - 0.446: 0 0.446 - 0.558: 3 Chirality restraints: 1664 Sorted by residual: 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 2.17 -2.73 -0.56 2.00e-01 2.50e+01 7.79e+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 2.17 -2.73 -0.56 2.00e-01 2.50e+01 7.76e+00 chirality pdb=" P G B 231 " pdb=" OP1 G B 231 " pdb=" OP2 G B 231 " pdb=" O5' G B 231 " both_signs ideal model delta sigma weight residual True 2.17 -2.66 -0.48 2.00e-01 2.50e+01 5.86e+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: 0.510 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.050 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 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= 0.194 Angle : 0.899 7.679 13152 Z= 0.404 Chirality : 0.109 0.558 1664 Planarity : 0.004 0.049 850 Dihedral : 21.372 166.189 3978 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/Z covalent geometry : bond 0.00341 / 0.19 ( 8922) covalent geometry : angle 0.89912 / 0.40 (13152) hydrogen bonds : bond 0.11402 / 7.31 ( 410) hydrogen bonds : angle 4.43012 / 3.23 ( 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 : 0.178 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: 0.0770 time to fit residues: 9.0813 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 : 0.198 ------------------------------------------------------------------------------- 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: 4.9990 chunk 53 optimal weight: 3.9990 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: 8.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS A 333 GLN A 370 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.168090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.133420 restraints weight = 18910.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.135477 restraints weight = 12500.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.138469 restraints weight = 7881.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.138124 restraints weight = 6426.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.138306 restraints weight = 6122.595| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.3535 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= 0.336 Angle : 1.354 18.602 13152 Z= 0.539 Chirality : 0.096 0.805 1664 Planarity : 0.006 0.044 850 Dihedral : 20.062 176.326 3142 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.62 % Allowed : 14.05 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.36 (0.38), residues: 446 helix: 1.41 (0.32), residues: 249 sheet: -1.11 (0.56), residues: 74 loop : -1.21 (0.50), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 17 TYR 0.026 0.003 TYR A 474 PHE 0.016 0.002 PHE A 313 TRP 0.018 0.002 TRP A 324 HIS 0.007 0.002 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00707 / 0.34 ( 8922) covalent geometry : angle 1.35416 / 0.54 (13152) hydrogen bonds : bond 0.06096 / 4.25 ( 410) hydrogen bonds : angle 4.37367 / 3.16 ( 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 70 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.213 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 67 average time/residue: 0.0682 time to fit residues: 7.1197 Evaluate side-chains 60 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR 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: 0.9990 chunk 57 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 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 = 0.4363 r_free = 0.4363 target = 0.171711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.136921 restraints weight = 18421.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.139612 restraints weight = 10978.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.142198 restraints weight = 7570.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.142238 restraints weight = 6120.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.142534 restraints weight = 5961.808| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8922 Z= 0.170 Angle : 1.033 10.718 13152 Z= 0.415 Chirality : 0.078 0.683 1664 Planarity : 0.004 0.040 850 Dihedral : 19.733 172.290 3142 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.70 % Allowed : 18.65 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.85 (0.39), residues: 446 helix: 1.81 (0.32), residues: 249 sheet: -0.77 (0.56), residues: 75 loop : -1.10 (0.53), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 391 TYR 0.024 0.003 TYR A 474 PHE 0.013 0.002 PHE A 328 TRP 0.018 0.002 TRP A 293 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 ( 8922) covalent geometry : angle 1.03325 / 0.42 (13152) hydrogen bonds : bond 0.04756 / 3.38 ( 410) hydrogen bonds : angle 3.84331 / 2.83 ( 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 72 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.8843 (m) cc_final: 0.8450 (p) REVERT: A 388 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7748 (mm-30) REVERT: A 551 MET cc_start: 0.5757 (ptm) cc_final: 0.5468 (ptm) outliers start: 10 outliers final: 6 residues processed: 70 average time/residue: 0.0791 time to fit residues: 8.1143 Evaluate side-chains 61 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 465 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 25 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 47 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 29 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 ASN ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.160160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.118962 restraints weight = 19427.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.122428 restraints weight = 9838.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.124416 restraints weight = 6919.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.125143 restraints weight = 5825.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.125143 restraints weight = 5441.547| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.5658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 8922 Z= 0.293 Angle : 1.252 14.648 13152 Z= 0.502 Chirality : 0.088 0.894 1664 Planarity : 0.005 0.041 850 Dihedral : 19.878 175.078 3142 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 6.76 % Allowed : 18.92 % 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 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: 0.07 (0.38), residues: 446 helix: 1.02 (0.32), residues: 249 sheet: -1.01 (0.61), residues: 64 loop : -1.14 (0.50), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 320 TYR 0.018 0.003 TYR A 91 PHE 0.016 0.002 PHE A 313 TRP 0.030 0.003 TRP A 21 HIS 0.005 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.29 ( 8922) covalent geometry : angle 1.25151 / 0.50 (13152) hydrogen bonds : bond 0.06280 / 4.42 ( 410) hydrogen bonds : angle 4.63961 / 3.34 ( 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 88 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 ARG cc_start: 0.7976 (mtt-85) cc_final: 0.7704 (mtt-85) REVERT: A 565 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7483 (tm-30) outliers start: 25 outliers final: 12 residues processed: 79 average time/residue: 0.0849 time to fit residues: 9.6882 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 : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 372 THR 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 559 ILE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 604 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 34 optimal weight: 0.6980 chunk 24 optimal weight: 30.0000 chunk 5 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4197 r_free = 0.4197 target = 0.157595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.123405 restraints weight = 19177.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.123906 restraints weight = 12844.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.125042 restraints weight = 10343.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.125439 restraints weight = 7586.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.125905 restraints weight = 7042.758| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.6518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 8922 Z= 0.294 Angle : 1.188 14.191 13152 Z= 0.479 Chirality : 0.084 0.872 1664 Planarity : 0.005 0.039 850 Dihedral : 19.883 165.528 3142 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 7.30 % Allowed : 22.16 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.04 (0.39), residues: 446 helix: 0.91 (0.32), residues: 250 sheet: -0.75 (0.63), residues: 63 loop : -1.34 (0.51), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 320 TYR 0.028 0.003 TYR A 91 PHE 0.018 0.002 PHE A 313 TRP 0.026 0.003 TRP A 21 HIS 0.006 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.29 ( 8922) covalent geometry : angle 1.18762 / 0.48 (13152) hydrogen bonds : bond 0.05710 / 4.03 ( 410) hydrogen bonds : angle 4.62777 / 3.38 ( 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 86 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: A 435 ARG cc_start: 0.8162 (mtt-85) cc_final: 0.7728 (mtt-85) REVERT: A 565 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7507 (tm-30) outliers start: 27 outliers final: 17 residues processed: 75 average time/residue: 0.0765 time to fit residues: 8.4694 Evaluate side-chains 69 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 90 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 303 VAL 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 429 ILE Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 489 ASN Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 583 VAL 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: 2.9990 chunk 23 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 60 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4201 r_free = 0.4201 target = 0.157800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.123264 restraints weight = 19065.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.124631 restraints weight = 12172.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.127227 restraints weight = 8501.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.127070 restraints weight = 6816.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.129501 restraints weight = 6760.509| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.6727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8922 Z= 0.250 Angle : 1.145 15.464 13152 Z= 0.461 Chirality : 0.081 0.782 1664 Planarity : 0.005 0.041 850 Dihedral : 19.795 171.451 3142 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 7.30 % Allowed : 23.51 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.02 (0.39), residues: 446 helix: 0.91 (0.32), residues: 250 sheet: -0.90 (0.62), residues: 65 loop : -1.20 (0.51), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 320 TYR 0.025 0.002 TYR A 91 PHE 0.014 0.002 PHE A 313 TRP 0.013 0.002 TRP A 324 HIS 0.004 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.25 ( 8922) covalent geometry : angle 1.14510 / 0.46 (13152) hydrogen bonds : bond 0.05596 / 3.97 ( 410) hydrogen bonds : angle 4.46504 / 3.25 ( 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 84 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7637 (mm-30) REVERT: A 435 ARG cc_start: 0.8078 (mtt-85) cc_final: 0.7606 (mtt-85) REVERT: A 565 GLN cc_start: 0.8093 (tm-30) cc_final: 0.7442 (tm-30) outliers start: 27 outliers final: 16 residues processed: 74 average time/residue: 0.0759 time to fit residues: 8.2963 Evaluate side-chains 70 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 64 GLN 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 372 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 489 ASN Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 604 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 16 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 ASN A 28 ASN A 342 HIS A 489 ASN A 496 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.163186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.127825 restraints weight = 19222.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.129320 restraints weight = 12081.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.130584 restraints weight = 9194.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.130742 restraints weight = 7389.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.131155 restraints weight = 6881.295| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.6540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8922 Z= 0.166 Angle : 1.040 16.726 13152 Z= 0.418 Chirality : 0.075 0.672 1664 Planarity : 0.004 0.040 850 Dihedral : 19.637 171.459 3142 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 5.41 % Allowed : 26.22 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.40 (0.39), residues: 446 helix: 1.27 (0.32), residues: 250 sheet: -0.74 (0.60), residues: 67 loop : -1.04 (0.51), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 391 TYR 0.021 0.002 TYR A 474 PHE 0.016 0.002 PHE A 328 TRP 0.016 0.002 TRP A 21 HIS 0.004 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 ( 8922) covalent geometry : angle 1.03964 / 0.42 (13152) hydrogen bonds : bond 0.04731 / 3.38 ( 410) hydrogen bonds : angle 4.08697 / 2.99 ( 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 80 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.8635 (m) cc_final: 0.8226 (p) REVERT: A 21 TRP cc_start: 0.8083 (t-100) cc_final: 0.7828 (t60) REVERT: A 324 TRP cc_start: 0.8225 (m100) cc_final: 0.7505 (m100) REVERT: A 435 ARG cc_start: 0.7855 (mtt-85) cc_final: 0.7527 (mtt-85) REVERT: A 452 SER cc_start: 0.7577 (t) cc_final: 0.7278 (p) REVERT: A 498 LEU cc_start: 0.8109 (tt) cc_final: 0.7840 (tp) outliers start: 20 outliers final: 10 residues processed: 70 average time/residue: 0.0804 time to fit residues: 8.2852 Evaluate side-chains 66 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 489 ASN Chi-restraints excluded: chain A residue 564 GLU 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: 5.9990 chunk 19 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 38 optimal weight: 0.0070 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4218 r_free = 0.4218 target = 0.159334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.124597 restraints weight = 18996.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.126076 restraints weight = 11544.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.128489 restraints weight = 8361.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.128542 restraints weight = 6669.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.131575 restraints weight = 6388.147| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.6865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8922 Z= 0.228 Angle : 1.102 16.212 13152 Z= 0.445 Chirality : 0.078 0.730 1664 Planarity : 0.004 0.039 850 Dihedral : 19.712 173.299 3142 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.41 % Allowed : 26.22 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.38 (0.39), residues: 446 helix: 1.20 (0.32), residues: 250 sheet: -0.84 (0.62), residues: 65 loop : -0.88 (0.51), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 391 TYR 0.040 0.003 TYR A 91 PHE 0.013 0.002 PHE A 313 TRP 0.012 0.001 TRP A 324 HIS 0.003 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.23 ( 8922) covalent geometry : angle 1.10239 / 0.44 (13152) hydrogen bonds : bond 0.05283 / 3.74 ( 410) hydrogen bonds : angle 4.35173 / 3.15 ( 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 69 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8142 (t-100) cc_final: 0.7836 (t60) REVERT: A 324 TRP cc_start: 0.8362 (m100) cc_final: 0.7524 (m100) REVERT: A 435 ARG cc_start: 0.8009 (mtt-85) cc_final: 0.7561 (mtt-85) REVERT: A 452 SER cc_start: 0.7779 (t) cc_final: 0.7447 (p) outliers start: 20 outliers final: 15 residues processed: 65 average time/residue: 0.0730 time to fit residues: 7.2149 Evaluate side-chains 63 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 90 ILE 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 377 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 489 ASN Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 604 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 40 optimal weight: 0.4980 chunk 37 optimal weight: 8.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 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 = 0.4210 r_free = 0.4210 target = 0.158431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.124485 restraints weight = 19112.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.124333 restraints weight = 14162.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.125790 restraints weight = 10638.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.126560 restraints weight = 7597.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.127254 restraints weight = 6954.740| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.7198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8922 Z= 0.240 Angle : 1.119 16.022 13152 Z= 0.453 Chirality : 0.079 0.752 1664 Planarity : 0.004 0.039 850 Dihedral : 19.874 174.539 3142 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.14 % Allowed : 26.76 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.32 (0.39), residues: 446 helix: 1.13 (0.32), residues: 250 sheet: -0.93 (0.63), residues: 65 loop : -0.81 (0.52), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 391 TYR 0.038 0.003 TYR A 91 PHE 0.013 0.002 PHE A 313 TRP 0.011 0.002 TRP A 21 HIS 0.004 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.24 ( 8922) covalent geometry : angle 1.11930 / 0.45 (13152) hydrogen bonds : bond 0.05397 / 3.81 ( 410) hydrogen bonds : angle 4.40567 / 3.19 ( 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 69 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8178 (t-100) cc_final: 0.7833 (t60) REVERT: A 324 TRP cc_start: 0.8322 (m100) cc_final: 0.7537 (m100) REVERT: A 405 MET cc_start: 0.3223 (mmm) cc_final: 0.2051 (mmp) REVERT: A 435 ARG cc_start: 0.7969 (mtt-85) cc_final: 0.7592 (mtt-85) REVERT: A 452 SER cc_start: 0.7722 (t) cc_final: 0.7470 (p) outliers start: 19 outliers final: 15 residues processed: 64 average time/residue: 0.0699 time to fit residues: 6.8075 Evaluate side-chains 65 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 90 ILE 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 377 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 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 55 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 12 optimal weight: 0.0870 chunk 6 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 36 optimal weight: 0.0970 chunk 22 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 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 = 0.4199 r_free = 0.4199 target = 0.157383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.122478 restraints weight = 18814.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.123948 restraints weight = 11745.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.126450 restraints weight = 8438.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.126374 restraints weight = 6750.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.126576 restraints weight = 6385.026| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.7484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8922 Z= 0.256 Angle : 1.140 12.888 13152 Z= 0.463 Chirality : 0.080 0.753 1664 Planarity : 0.005 0.069 850 Dihedral : 19.911 175.087 3142 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.59 % Allowed : 27.03 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.22 (0.39), residues: 446 helix: 1.01 (0.32), residues: 250 sheet: -0.99 (0.63), residues: 65 loop : -0.76 (0.52), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 391 TYR 0.028 0.003 TYR A 91 PHE 0.014 0.002 PHE A 313 TRP 0.011 0.002 TRP A 382 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.26 ( 8922) covalent geometry : angle 1.13980 / 0.46 (13152) hydrogen bonds : bond 0.05650 / 3.96 ( 410) hydrogen bonds : angle 4.50939 / 3.27 ( 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 67 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8198 (t-100) cc_final: 0.7834 (t60) REVERT: A 34 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8012 (tt0) REVERT: A 391 ARG cc_start: 0.8168 (ptt90) cc_final: 0.7963 (ptt90) REVERT: A 405 MET cc_start: 0.3204 (mmm) cc_final: 0.1924 (mmp) REVERT: A 435 ARG cc_start: 0.8028 (mtt-85) cc_final: 0.7597 (mtt-85) REVERT: A 452 SER cc_start: 0.7831 (t) cc_final: 0.7497 (p) outliers start: 17 outliers final: 16 residues processed: 63 average time/residue: 0.0655 time to fit residues: 6.2188 Evaluate side-chains 64 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.199 ------------------------------------------------------------------------------- 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 64 GLN Chi-restraints excluded: chain A residue 90 ILE 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 377 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 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 43 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 0.0770 chunk 22 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 overall best weight: 2.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.158549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.124202 restraints weight = 18534.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.126692 restraints weight = 11081.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.127227 restraints weight = 8425.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.127584 restraints weight = 6800.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.127933 restraints weight = 6391.530| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.7576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8922 Z= 0.227 Angle : 1.093 13.427 13152 Z= 0.445 Chirality : 0.077 0.707 1664 Planarity : 0.005 0.054 850 Dihedral : 19.874 174.671 3142 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 5.68 % Allowed : 26.22 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.37 (0.39), residues: 446 helix: 1.15 (0.32), residues: 250 sheet: -1.01 (0.63), residues: 65 loop : -0.68 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 391 TYR 0.028 0.002 TYR A 91 PHE 0.012 0.002 PHE A 313 TRP 0.015 0.002 TRP A 382 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.23 ( 8922) covalent geometry : angle 1.09271 / 0.44 (13152) hydrogen bonds : bond 0.05320 / 3.78 ( 410) hydrogen bonds : angle 4.38506 / 3.19 ( 1005) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1275.88 seconds wall clock time: 22 minutes 54.34 seconds (1374.34 seconds total)