Starting phenix.real_space_refine on Thu Jul 2 10:37:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7n3o_24142/07_2026/7n3o_24142.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n3o_24142/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7n3o_24142/07_2026/7n3o_24142.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7n3o_24142/07_2026/7n3o_24142.cif" model { file = "/net/cci-nas-00/data/ceres_data/7n3o_24142/07_2026/7n3o_24142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n3o_24142/07_2026/7n3o_24142.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n3o_24142/07_2026/7n3o_24142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n3o_24142/07_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-6108/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: {'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: 1.31, per 1000 atoms: 0.16 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: 0.54 Conformation dependent library (CDL) restraints added in 213.1 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: 1.09 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: 1.17 Time building geometry restraints manager: 0.74 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: 4638 35.84 - 71.67: 170 71.67 - 107.51: 16 107.51 - 143.34: 4 143.34 - 179.18: 8 Dihedral angle restraints: 4836 sinusoidal: 3513 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 4833 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: 0.450 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.710 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: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.480 ------------------------------------------------------------------------------- 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= 0.175 Angle : 0.594 7.679 13152 Z= 0.336 Chirality : 0.038 0.338 1664 Planarity : 0.004 0.049 850 Dihedral : 17.141 179.181 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 0.00289 / 0.17 ( 8922) covalent geometry : angle 0.59407 / 0.34 (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 : 0.154 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: 0.0588 time to fit residues: 6.9211 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 : 0.150 ------------------------------------------------------------------------------- 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... ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS A 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.161549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.126009 restraints weight = 18968.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.128020 restraints weight = 12599.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.129163 restraints weight = 8894.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.129290 restraints weight = 7172.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.129804 restraints weight = 6620.915| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 8922 Z= 0.348 Angle : 0.873 10.053 13152 Z= 0.433 Chirality : 0.045 0.251 1664 Planarity : 0.006 0.038 850 Dihedral : 17.262 175.820 3142 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.16 % Allowed : 15.68 % 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: -0.09 (0.38), residues: 446 helix: 0.91 (0.31), residues: 250 sheet: -1.00 (0.58), residues: 74 loop : -1.32 (0.50), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 17 TYR 0.024 0.003 TYR A 316 PHE 0.017 0.003 PHE A 567 TRP 0.022 0.003 TRP A 324 HIS 0.011 0.002 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00710 / 0.35 ( 8922) covalent geometry : angle 0.87327 / 0.43 (13152) hydrogen bonds : bond 0.06491 / 4.48 ( 410) hydrogen bonds : angle 4.76775 / 3.44 ( 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 76 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.118 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 73 average time/residue: 0.0741 time to fit residues: 7.5120 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 : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 CYS 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: 0.7980 chunk 57 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4312 r_free = 0.4312 target = 0.167242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.132802 restraints weight = 18246.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.134358 restraints weight = 11600.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.135482 restraints weight = 8381.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.135629 restraints weight = 6930.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.135966 restraints weight = 6259.555| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.4002 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= 0.134 Angle : 0.620 9.810 13152 Z= 0.312 Chirality : 0.035 0.236 1664 Planarity : 0.004 0.043 850 Dihedral : 16.745 175.872 3142 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.43 % Allowed : 19.73 % Favored : 77.84 % 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: 0.67 (0.39), residues: 446 helix: 1.59 (0.32), residues: 249 sheet: -0.63 (0.58), residues: 75 loop : -1.17 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 391 TYR 0.016 0.002 TYR A 570 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/Z covalent geometry : bond 0.00274 / 0.13 ( 8922) covalent geometry : angle 0.61966 / 0.31 (13152) hydrogen bonds : bond 0.04337 / 3.05 ( 410) hydrogen bonds : angle 3.96117 / 2.92 ( 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 75 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5465 (ppp) cc_final: 0.5149 (ppp) REVERT: A 21 TRP cc_start: 0.8007 (t-100) cc_final: 0.7728 (t60) REVERT: A 565 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7699 (tm-30) outliers start: 9 outliers final: 5 residues processed: 71 average time/residue: 0.0596 time to fit residues: 6.1418 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 : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 305 PHE 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: 9.9990 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 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: 4.5990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 HIS A 379 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.154779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.113513 restraints weight = 19299.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.116842 restraints weight = 9580.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.118853 restraints weight = 6743.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.119754 restraints weight = 5709.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.120112 restraints weight = 5294.723| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.5924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 8922 Z= 0.341 Angle : 0.855 12.053 13152 Z= 0.427 Chirality : 0.045 0.262 1664 Planarity : 0.006 0.045 850 Dihedral : 17.576 178.538 3142 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 7.84 % Allowed : 19.19 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.79 (0.31), residues: 250 sheet: -0.69 (0.61), residues: 61 loop : -1.46 (0.50), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 320 TYR 0.019 0.003 TYR A 91 PHE 0.015 0.003 PHE A 313 TRP 0.018 0.002 TRP A 324 HIS 0.006 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.34 ( 8922) covalent geometry : angle 0.85539 / 0.43 (13152) hydrogen bonds : bond 0.06597 / 4.60 ( 410) hydrogen bonds : angle 4.88988 / 3.56 ( 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: 29 poor density : 59 time to evaluate : 0.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8332 (t-100) cc_final: 0.7890 (t60) REVERT: A 405 MET cc_start: 0.2383 (mmt) cc_final: 0.0882 (mmp) REVERT: A 565 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7523 (tm-30) REVERT: A 613 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7465 (tp-100) outliers start: 29 outliers final: 14 residues processed: 78 average time/residue: 0.0474 time to fit residues: 5.6318 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 : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 379 ASN 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 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: 0.9990 chunk 54 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 31 optimal weight: 0.5980 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 342 HIS A 496 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.156627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.121234 restraints weight = 18794.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.122035 restraints weight = 11199.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.123487 restraints weight = 8559.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.123624 restraints weight = 6935.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.123805 restraints weight = 6748.310| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.6036 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= 0.223 Angle : 0.705 15.012 13152 Z= 0.356 Chirality : 0.039 0.233 1664 Planarity : 0.005 0.046 850 Dihedral : 17.446 179.472 3142 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 6.22 % Allowed : 22.43 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.39), residues: 446 helix: 1.10 (0.32), residues: 250 sheet: -0.51 (0.65), residues: 65 loop : -1.24 (0.50), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 391 TYR 0.032 0.003 TYR A 570 PHE 0.011 0.002 PHE A 313 TRP 0.013 0.002 TRP A 324 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.22 ( 8922) covalent geometry : angle 0.70502 / 0.36 (13152) hydrogen bonds : bond 0.05158 / 3.65 ( 410) hydrogen bonds : angle 4.41043 / 3.24 ( 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 81 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 58 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8218 (t-100) cc_final: 0.7887 (t60) REVERT: A 565 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7464 (tm-30) outliers start: 23 outliers final: 16 residues processed: 75 average time/residue: 0.0621 time to fit residues: 7.2511 Evaluate side-chains 72 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 303 VAL 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 381 LEU 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 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: 6.9990 chunk 23 optimal weight: 30.0000 chunk 44 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 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 = 0.4173 r_free = 0.4173 target = 0.155517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.120302 restraints weight = 18877.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.120399 restraints weight = 11375.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.121062 restraints weight = 9447.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.123516 restraints weight = 7591.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.123202 restraints weight = 6740.521| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.6402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8922 Z= 0.220 Angle : 0.701 15.785 13152 Z= 0.353 Chirality : 0.039 0.232 1664 Planarity : 0.005 0.045 850 Dihedral : 17.448 179.920 3142 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 7.03 % Allowed : 24.05 % Favored : 68.92 % 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: 0.28 (0.39), residues: 446 helix: 1.14 (0.32), residues: 250 sheet: -0.43 (0.66), residues: 58 loop : -1.23 (0.49), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 391 TYR 0.031 0.002 TYR A 570 PHE 0.013 0.002 PHE A 313 TRP 0.016 0.001 TRP A 324 HIS 0.005 0.002 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.22 ( 8922) covalent geometry : angle 0.70136 / 0.35 (13152) hydrogen bonds : bond 0.05211 / 3.66 ( 410) hydrogen bonds : angle 4.44152 / 3.26 ( 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: 26 poor density : 58 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8247 (t-100) cc_final: 0.7962 (t60) REVERT: A 565 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7445 (tm-30) outliers start: 26 outliers final: 19 residues processed: 77 average time/residue: 0.0623 time to fit residues: 7.4712 Evaluate side-chains 75 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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 90 ILE Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 373 LEU 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 16 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 chunk 12 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.160559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.126644 restraints weight = 18895.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.125537 restraints weight = 13721.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.127146 restraints weight = 10069.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.127595 restraints weight = 7531.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.127940 restraints weight = 6976.359| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.6131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8922 Z= 0.128 Angle : 0.628 16.743 13152 Z= 0.314 Chirality : 0.034 0.222 1664 Planarity : 0.004 0.041 850 Dihedral : 17.160 178.470 3142 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 6.22 % Allowed : 25.41 % 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: 0.80 (0.40), residues: 446 helix: 1.56 (0.33), residues: 250 sheet: -0.65 (0.60), residues: 72 loop : -0.75 (0.54), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 391 TYR 0.034 0.002 TYR A 570 PHE 0.019 0.002 PHE A 328 TRP 0.018 0.002 TRP A 324 HIS 0.005 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 ( 8922) covalent geometry : angle 0.62842 / 0.31 (13152) hydrogen bonds : bond 0.04211 / 2.99 ( 410) hydrogen bonds : angle 3.95562 / 2.92 ( 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 84 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8104 (t-100) cc_final: 0.7822 (t60) REVERT: A 280 PRO cc_start: 0.8378 (Cg_exo) cc_final: 0.7946 (Cg_endo) REVERT: A 498 LEU cc_start: 0.8081 (tt) cc_final: 0.7828 (tp) outliers start: 23 outliers final: 12 residues processed: 77 average time/residue: 0.0606 time to fit residues: 7.2950 Evaluate side-chains 68 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.113 ------------------------------------------------------------------------------- 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 303 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 604 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 13 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.160884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.120082 restraints weight = 18632.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.123478 restraints weight = 9393.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.125629 restraints weight = 6609.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.126559 restraints weight = 5546.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.126833 restraints weight = 5132.656| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.6109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8922 Z= 0.127 Angle : 0.612 15.099 13152 Z= 0.305 Chirality : 0.033 0.222 1664 Planarity : 0.004 0.040 850 Dihedral : 16.979 178.376 3142 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.78 % Allowed : 27.03 % 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: 0.98 (0.40), residues: 446 helix: 1.73 (0.32), residues: 250 sheet: -0.52 (0.62), residues: 65 loop : -0.77 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 391 TYR 0.034 0.002 TYR A 570 PHE 0.016 0.001 PHE A 328 TRP 0.012 0.001 TRP A 324 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 ( 8922) covalent geometry : angle 0.61174 / 0.31 (13152) hydrogen bonds : bond 0.04245 / 3.00 ( 410) hydrogen bonds : angle 3.85946 / 2.84 ( 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 71 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 LEU cc_start: 0.8031 (tt) cc_final: 0.7816 (tp) REVERT: A 625 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7845 (tm-30) outliers start: 14 outliers final: 14 residues processed: 68 average time/residue: 0.0688 time to fit residues: 7.1869 Evaluate side-chains 69 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 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 321 GLN Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 604 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 0.0970 chunk 3 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.159367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.124304 restraints weight = 18829.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.124402 restraints weight = 11750.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.126398 restraints weight = 9637.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.126384 restraints weight = 7254.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.126675 restraints weight = 6848.626| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.6286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8922 Z= 0.164 Angle : 0.646 14.177 13152 Z= 0.323 Chirality : 0.035 0.231 1664 Planarity : 0.004 0.040 850 Dihedral : 16.990 178.459 3142 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.32 % Allowed : 27.84 % Favored : 67.84 % 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: 0.91 (0.39), residues: 446 helix: 1.63 (0.32), residues: 250 sheet: -0.50 (0.62), residues: 65 loop : -0.74 (0.52), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 391 TYR 0.033 0.002 TYR A 570 PHE 0.012 0.002 PHE A 328 TRP 0.032 0.002 TRP A 21 HIS 0.005 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 ( 8922) covalent geometry : angle 0.64597 / 0.32 (13152) hydrogen bonds : bond 0.04411 / 3.09 ( 410) hydrogen bonds : angle 4.00066 / 2.93 ( 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 73 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8052 (tt0) REVERT: A 625 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7865 (tm-30) outliers start: 16 outliers final: 14 residues processed: 68 average time/residue: 0.0685 time to fit residues: 7.2090 Evaluate side-chains 69 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 321 GLN Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 604 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 55 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.160243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.118928 restraints weight = 18586.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.122272 restraints weight = 9385.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.124444 restraints weight = 6645.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.125195 restraints weight = 5596.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.125195 restraints weight = 5209.535| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.6287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8922 Z= 0.141 Angle : 0.634 14.640 13152 Z= 0.316 Chirality : 0.034 0.227 1664 Planarity : 0.004 0.039 850 Dihedral : 16.927 178.042 3142 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.59 % Allowed : 28.65 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.96 (0.39), residues: 446 helix: 1.62 (0.32), residues: 250 sheet: -0.42 (0.63), residues: 65 loop : -0.61 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 391 TYR 0.035 0.002 TYR A 570 PHE 0.015 0.001 PHE A 328 TRP 0.033 0.002 TRP A 21 HIS 0.005 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 ( 8922) covalent geometry : angle 0.63369 / 0.32 (13152) hydrogen bonds : bond 0.04228 / 2.97 ( 410) hydrogen bonds : angle 3.93973 / 2.89 ( 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 73 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8167 (tt0) REVERT: A 391 ARG cc_start: 0.8486 (ptt90) cc_final: 0.8231 (ptt90) REVERT: A 625 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7834 (tm-30) outliers start: 17 outliers final: 15 residues processed: 70 average time/residue: 0.0643 time to fit residues: 7.0746 Evaluate side-chains 72 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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 303 VAL 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 321 GLN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 604 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 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: 0.3980 chunk 22 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 28 optimal weight: 0.0970 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.156109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.120450 restraints weight = 18658.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.120590 restraints weight = 11641.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.121878 restraints weight = 9508.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.122462 restraints weight = 7199.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.123842 restraints weight = 7424.537| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.6794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8922 Z= 0.212 Angle : 0.695 12.995 13152 Z= 0.351 Chirality : 0.038 0.233 1664 Planarity : 0.004 0.041 850 Dihedral : 17.244 179.258 3142 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.59 % Allowed : 28.92 % 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: 0.65 (0.39), residues: 446 helix: 1.31 (0.32), residues: 250 sheet: -0.43 (0.62), residues: 65 loop : -0.69 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 391 TYR 0.034 0.002 TYR A 570 PHE 0.015 0.002 PHE A 281 TRP 0.025 0.002 TRP A 21 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.21 ( 8922) covalent geometry : angle 0.69511 / 0.35 (13152) hydrogen bonds : bond 0.04763 / 3.30 ( 410) hydrogen bonds : angle 4.27638 / 3.15 ( 1005) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1231.70 seconds wall clock time: 22 minutes 6.04 seconds (1326.04 seconds total)