Starting phenix.real_space_refine on Tue Aug 4 14:34:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6s_62134/08_2026/9k6s_62134.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6s_62134/08_2026/9k6s_62134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k6s_62134/08_2026/9k6s_62134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6s_62134/08_2026/9k6s_62134.map" model { file = "/net/cci-nas-00/data/ceres_data/9k6s_62134/08_2026/9k6s_62134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6s_62134/08_2026/9k6s_62134.cif" } resolution = 2.8 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= -0.000 sd= 0.041 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: 6 Type Number sf(0) Gaussians P 38 5.49 5 Mg 1 5.21 5 S 19 5.16 5 C 2482 2.51 5 N 744 2.21 5 O 854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4138 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3332 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 25, 'TRANS': 395} Chain breaks: 2 Chain: "B" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 401 Classifications: {'RNA': 19} Modifications used: {'p5*END': 1, 'rna2p_pyr': 3, 'rna3p_pur': 8, 'rna3p_pyr': 8} Link IDs: {'rna2p': 3, 'rna3p': 15} Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 404 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 9, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 15} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.21, per 1000 atoms: 0.29 Number of scatterers: 4138 At special positions: 0 Unit cell: (66.12, 77.52, 87.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 19 16.00 P 38 15.00 Mg 1 11.99 O 854 8.00 N 744 7.00 C 2482 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: 0.38 Conformation dependent library (CDL) restraints added in 126.8 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 788 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 2 sheets defined 35.4% alpha, 11.6% beta 13 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 463 through 481 Processing helix chain 'A' and resid 500 through 510 removed outlier: 3.954A pdb=" N MET A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 538 removed outlier: 4.178A pdb=" N ALA A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 removed outlier: 3.571A pdb=" N GLN A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG A 554 " --> pdb=" O LYS A 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 549 through 554' Processing helix chain 'A' and resid 556 through 572 removed outlier: 3.721A pdb=" N GLY A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 589 Processing helix chain 'A' and resid 641 through 658 removed outlier: 3.595A pdb=" N MET A 645 " --> pdb=" O ASP A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 680 removed outlier: 3.522A pdb=" N GLN A 675 " --> pdb=" O SER A 672 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A 676 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLN A 677 " --> pdb=" O GLY A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 693 removed outlier: 3.695A pdb=" N LYS A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 789 Processing helix chain 'A' and resid 800 through 815 Processing helix chain 'A' and resid 840 through 846 Processing sheet with id=AA1, first strand: chain 'A' and resid 491 through 494 removed outlier: 4.191A pdb=" N LYS A 493 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ALA A 452 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ILE A 521 " --> pdb=" O ALA A 452 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ALA A 454 " --> pdb=" O ILE A 521 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 625 through 632 removed outlier: 5.600A pdb=" N PHE A 593 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE A 664 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ILE A 705 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N PHE A 666 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL A 707 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ARG A 668 " --> pdb=" O VAL A 707 " (cutoff:3.500A) 121 hydrogen bonds defined for protein. 339 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 0.42 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1078 1.34 - 1.45: 972 1.45 - 1.57: 2156 1.57 - 1.69: 74 1.69 - 1.81: 27 Bond restraints: 4307 Sorted by residual: bond pdb=" C GLU A 502 " pdb=" N PRO A 503 " ideal model delta sigma weight residual 1.336 1.375 -0.039 1.20e-02 6.94e+03 1.06e+01 bond pdb=" N VAL A 707 " pdb=" CA VAL A 707 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.14e-02 7.69e+03 9.09e+00 bond pdb=" N GLN A 633 " pdb=" CA GLN A 633 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.23e-02 6.61e+03 7.52e+00 bond pdb=" N ASP A 597 " pdb=" CA ASP A 597 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.21e-02 6.83e+03 7.26e+00 bond pdb=" P U B 13 " pdb=" O5' U B 13 " ideal model delta sigma weight residual 1.593 1.619 -0.026 1.00e-02 1.00e+04 6.71e+00 ... (remaining 4302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 5628 1.82 - 3.64: 325 3.64 - 5.46: 31 5.46 - 7.28: 26 7.28 - 9.10: 7 Bond angle restraints: 6017 Sorted by residual: angle pdb=" N1 C C 14 " pdb=" C2 C C 14 " pdb=" O2 C C 14 " ideal model delta sigma weight residual 118.90 122.23 -3.33 6.00e-01 2.78e+00 3.08e+01 angle pdb=" O2 C C 14 " pdb=" C2 C C 14 " pdb=" N3 C C 14 " ideal model delta sigma weight residual 121.90 118.10 3.80 7.00e-01 2.04e+00 2.95e+01 angle pdb=" C4' U B 12 " pdb=" O4' U B 12 " pdb=" C1' U B 12 " ideal model delta sigma weight residual 109.70 106.11 3.59 7.00e-01 2.04e+00 2.63e+01 angle pdb=" N VAL A 552 " pdb=" CA VAL A 552 " pdb=" C VAL A 552 " ideal model delta sigma weight residual 112.96 108.09 4.87 1.00e+00 1.00e+00 2.38e+01 angle pdb=" C1' U C 20 " pdb=" N1 U C 20 " pdb=" C2 U C 20 " ideal model delta sigma weight residual 117.70 123.49 -5.79 1.20e+00 6.94e-01 2.33e+01 ... (remaining 6012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.92: 2371 30.92 - 61.83: 222 61.83 - 92.74: 39 92.74 - 123.66: 1 123.66 - 154.57: 2 Dihedral angle restraints: 2635 sinusoidal: 1413 harmonic: 1222 Sorted by residual: dihedral pdb=" O4' U C 20 " pdb=" C1' U C 20 " pdb=" N1 U C 20 " pdb=" C2 U C 20 " ideal model delta sinusoidal sigma weight residual 200.00 45.43 154.57 1 1.50e+01 4.44e-03 8.12e+01 dihedral pdb=" C5' U B 12 " pdb=" C4' U B 12 " pdb=" C3' U B 12 " pdb=" O3' U B 12 " ideal model delta sinusoidal sigma weight residual 147.00 94.76 52.24 1 8.00e+00 1.56e-02 5.82e+01 dihedral pdb=" O4' U B 12 " pdb=" C4' U B 12 " pdb=" C3' U B 12 " pdb=" C2' U B 12 " ideal model delta sinusoidal sigma weight residual 24.00 -23.29 47.29 1 8.00e+00 1.56e-02 4.83e+01 ... (remaining 2632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 635 0.109 - 0.219: 62 0.219 - 0.328: 2 0.328 - 0.438: 1 0.438 - 0.547: 7 Chirality restraints: 707 Sorted by residual: chirality pdb=" P U B 12 " pdb=" OP1 U B 12 " pdb=" OP2 U B 12 " pdb=" O5' U B 12 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.48e+00 chirality pdb=" P U B 13 " pdb=" OP1 U B 13 " pdb=" OP2 U B 13 " pdb=" O5' U B 13 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.76e+00 chirality pdb=" P U B 11 " pdb=" OP1 U B 11 " pdb=" OP2 U B 11 " pdb=" O5' U B 11 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.48e+00 ... (remaining 704 not shown) Planarity restraints: 635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 814 " 0.867 9.50e-02 1.11e+02 3.89e-01 9.17e+01 pdb=" NE ARG A 814 " -0.052 2.00e-02 2.50e+03 pdb=" CZ ARG A 814 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 814 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 814 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 761 " -0.803 9.50e-02 1.11e+02 3.60e-01 7.89e+01 pdb=" NE ARG A 761 " 0.048 2.00e-02 2.50e+03 pdb=" CZ ARG A 761 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 761 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 761 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 710 " -0.205 9.50e-02 1.11e+02 9.17e-02 5.17e+00 pdb=" NE ARG A 710 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 710 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 710 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 710 " -0.007 2.00e-02 2.50e+03 ... (remaining 632 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 676 2.77 - 3.30: 3832 3.30 - 3.83: 7769 3.83 - 4.37: 8990 4.37 - 4.90: 13974 Nonbonded interactions: 35241 Sorted by model distance: nonbonded pdb=" OH TYR A 804 " pdb=" OP1 A B 5 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR A 765 " pdb=" O SER A 798 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR A 538 " pdb=" O GLN A 847 " model vdw 2.309 3.040 nonbonded pdb=" O GLN A 785 " pdb=" OG1 THR A 789 " model vdw 2.313 3.040 nonbonded pdb=" OG1 THR A 556 " pdb=" OG1 THR A 559 " model vdw 2.319 3.040 ... (remaining 35236 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 individual isotropic 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: 0.280 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 4.990 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4935 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 : 0.005 0.039 4307 Z= 0.326 Angle : 0.975 9.105 6017 Z= 0.623 Chirality : 0.080 0.547 707 Planarity : 0.022 0.389 635 Dihedral : 22.124 154.571 1847 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.30 % Favored : 94.22 % Rotamer: Outliers : 2.49 % Allowed : 30.19 % Favored : 67.31 % 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: -1.58 (0.41), residues: 415 helix: -0.54 (0.41), residues: 145 sheet: -1.32 (0.58), residues: 81 loop : -1.20 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 624 TYR 0.033 0.002 TYR A 815 PHE 0.011 0.002 PHE A 653 TRP 0.008 0.001 TRP A 435 HIS 0.008 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.33 ( 4307) covalent geometry : angle 0.97455 / 0.62 ( 6017) hydrogen bonds : bond 0.13169 / 8.85 ( 153) hydrogen bonds : angle 7.30653 / 5.01 ( 399) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 437 MET cc_start: 0.4543 (ttp) cc_final: 0.3784 (tpt) REVERT: A 545 GLN cc_start: 0.4820 (tp40) cc_final: 0.4529 (tp-100) REVERT: A 761 ARG cc_start: 0.3122 (OUTLIER) cc_final: 0.0422 (mmm160) outliers start: 9 outliers final: 1 residues processed: 69 average time/residue: 0.6387 time to fit residues: 45.4637 Evaluate side-chains 45 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ARG Chi-restraints excluded: chain A residue 761 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.0980 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 0.0670 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 ASN A 562 ASN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 HIS A 839 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5212 r_free = 0.5212 target = 0.296346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.257574 restraints weight = 4635.588| |-----------------------------------------------------------------------------| r_work (start): 0.4929 rms_B_bonded: 2.21 r_work: 0.4829 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4928 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4307 Z= 0.139 Angle : 0.626 7.313 6017 Z= 0.330 Chirality : 0.044 0.224 707 Planarity : 0.005 0.060 635 Dihedral : 21.080 152.171 1047 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 6.09 % Allowed : 29.36 % Favored : 64.54 % 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: -1.15 (0.42), residues: 415 helix: 0.10 (0.43), residues: 144 sheet: -1.33 (0.56), residues: 79 loop : -1.09 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 814 TYR 0.007 0.001 TYR A 749 PHE 0.019 0.002 PHE A 811 TRP 0.006 0.001 TRP A 435 HIS 0.011 0.002 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 4307) covalent geometry : angle 0.62572 / 0.33 ( 6017) hydrogen bonds : bond 0.05646 / 3.42 ( 153) hydrogen bonds : angle 5.76509 / 4.03 ( 399) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.077 Fit side-chains revert: symmetry clash REVERT: A 490 CYS cc_start: 0.2777 (OUTLIER) cc_final: 0.1702 (p) REVERT: A 663 ARG cc_start: 0.5265 (mpt-90) cc_final: 0.4978 (mmm-85) REVERT: A 666 PHE cc_start: 0.4990 (t80) cc_final: 0.4404 (t80) REVERT: A 697 ASP cc_start: 0.5618 (OUTLIER) cc_final: 0.5089 (m-30) REVERT: A 710 ARG cc_start: 0.4275 (OUTLIER) cc_final: 0.2796 (tmt-80) REVERT: A 804 TYR cc_start: 0.7172 (OUTLIER) cc_final: 0.6224 (m-80) outliers start: 22 outliers final: 3 residues processed: 66 average time/residue: 0.4845 time to fit residues: 33.1545 Evaluate side-chains 48 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 710 ARG Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 804 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 2 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 7 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 ASN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 HIS A 839 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5192 r_free = 0.5192 target = 0.293582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.253553 restraints weight = 4627.486| |-----------------------------------------------------------------------------| r_work (start): 0.4895 rms_B_bonded: 2.23 r_work: 0.4793 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5046 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4307 Z= 0.137 Angle : 0.597 5.696 6017 Z= 0.319 Chirality : 0.043 0.232 707 Planarity : 0.005 0.036 635 Dihedral : 20.938 152.185 1043 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 6.65 % Allowed : 29.92 % Favored : 63.43 % 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 (0.42), residues: 415 helix: 0.27 (0.42), residues: 145 sheet: -1.28 (0.55), residues: 79 loop : -0.99 (0.48), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 423 TYR 0.020 0.002 TYR A 698 PHE 0.021 0.002 PHE A 811 TRP 0.005 0.001 TRP A 435 HIS 0.009 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 4307) covalent geometry : angle 0.59722 / 0.32 ( 6017) hydrogen bonds : bond 0.05458 / 3.17 ( 153) hydrogen bonds : angle 5.45749 / 3.84 ( 399) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 46 time to evaluate : 0.094 Fit side-chains REVERT: A 490 CYS cc_start: 0.2995 (OUTLIER) cc_final: 0.2015 (p) REVERT: A 663 ARG cc_start: 0.5365 (mpt-90) cc_final: 0.5009 (mmm-85) REVERT: A 666 PHE cc_start: 0.5178 (t80) cc_final: 0.4692 (t80) REVERT: A 710 ARG cc_start: 0.4551 (OUTLIER) cc_final: 0.2951 (tmt-80) outliers start: 24 outliers final: 4 residues processed: 62 average time/residue: 0.5534 time to fit residues: 35.5948 Evaluate side-chains 44 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 710 ARG Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 818 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 19 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 ASN A 548 GLN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN A 764 HIS A 807 HIS A 839 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5191 r_free = 0.5191 target = 0.291345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.252705 restraints weight = 4547.052| |-----------------------------------------------------------------------------| r_work (start): 0.4908 rms_B_bonded: 2.11 r_work: 0.4808 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5117 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4307 Z= 0.133 Angle : 0.595 6.091 6017 Z= 0.314 Chirality : 0.044 0.254 707 Planarity : 0.004 0.034 635 Dihedral : 20.848 152.198 1043 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 6.65 % Allowed : 27.98 % Favored : 65.37 % 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: -0.94 (0.42), residues: 415 helix: 0.33 (0.43), residues: 146 sheet: -1.17 (0.56), residues: 79 loop : -1.04 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 423 TYR 0.013 0.002 TYR A 784 PHE 0.018 0.002 PHE A 811 TRP 0.005 0.001 TRP A 769 HIS 0.008 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 4307) covalent geometry : angle 0.59458 / 0.31 ( 6017) hydrogen bonds : bond 0.05302 / 3.09 ( 153) hydrogen bonds : angle 5.34593 / 3.79 ( 399) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 42 time to evaluate : 0.087 Fit side-chains REVERT: A 490 CYS cc_start: 0.3095 (OUTLIER) cc_final: 0.2159 (p) REVERT: A 549 MET cc_start: 0.6716 (OUTLIER) cc_final: 0.6247 (ptm) REVERT: A 639 ILE cc_start: 0.4405 (OUTLIER) cc_final: 0.4037 (mm) REVERT: A 663 ARG cc_start: 0.5215 (mpt-90) cc_final: 0.4820 (mmm-85) REVERT: A 666 PHE cc_start: 0.5363 (t80) cc_final: 0.4999 (t80) REVERT: A 689 GLU cc_start: 0.5338 (OUTLIER) cc_final: 0.4912 (tm-30) outliers start: 24 outliers final: 2 residues processed: 60 average time/residue: 0.4740 time to fit residues: 29.6076 Evaluate side-chains 46 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 738 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 43 optimal weight: 50.0000 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 ASN A 548 GLN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN A 600 HIS ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 772 ASN A 839 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5116 r_free = 0.5116 target = 0.280860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.239503 restraints weight = 4479.543| |-----------------------------------------------------------------------------| r_work (start): 0.4825 rms_B_bonded: 2.13 r_work: 0.4722 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5384 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 4307 Z= 0.242 Angle : 0.724 9.200 6017 Z= 0.379 Chirality : 0.049 0.268 707 Planarity : 0.005 0.044 635 Dihedral : 20.824 151.550 1039 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.27 % Favored : 93.49 % Rotamer: Outliers : 6.93 % Allowed : 28.81 % Favored : 64.27 % 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: -1.13 (0.41), residues: 415 helix: 0.01 (0.42), residues: 147 sheet: -1.22 (0.55), residues: 81 loop : -1.04 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 814 TYR 0.013 0.003 TYR A 749 PHE 0.028 0.003 PHE A 811 TRP 0.005 0.002 TRP A 451 HIS 0.015 0.002 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.24 ( 4307) covalent geometry : angle 0.72379 / 0.38 ( 6017) hydrogen bonds : bond 0.06578 / 3.70 ( 153) hydrogen bonds : angle 5.42772 / 3.85 ( 399) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 42 time to evaluate : 0.147 Fit side-chains REVERT: A 505 PHE cc_start: 0.5517 (OUTLIER) cc_final: 0.4644 (t80) REVERT: A 542 MET cc_start: 0.5258 (pmm) cc_final: 0.4223 (ptp) REVERT: A 639 ILE cc_start: 0.4386 (OUTLIER) cc_final: 0.3906 (mm) REVERT: A 702 ILE cc_start: 0.5500 (OUTLIER) cc_final: 0.5012 (mt) outliers start: 25 outliers final: 6 residues processed: 64 average time/residue: 0.4176 time to fit residues: 27.8272 Evaluate side-chains 49 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 738 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.0870 chunk 11 optimal weight: 0.6980 chunk 26 optimal weight: 0.0270 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 548 GLN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5171 r_free = 0.5171 target = 0.286542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.246882 restraints weight = 4516.386| |-----------------------------------------------------------------------------| r_work (start): 0.4858 rms_B_bonded: 1.97 r_work: 0.4718 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5396 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4307 Z= 0.134 Angle : 0.615 7.216 6017 Z= 0.323 Chirality : 0.044 0.237 707 Planarity : 0.004 0.036 635 Dihedral : 20.728 153.302 1039 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.71 % Allowed : 31.58 % Favored : 63.71 % 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: -0.87 (0.42), residues: 415 helix: 0.45 (0.43), residues: 146 sheet: -1.16 (0.55), residues: 81 loop : -1.04 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 423 TYR 0.010 0.002 TYR A 765 PHE 0.015 0.002 PHE A 811 TRP 0.004 0.001 TRP A 769 HIS 0.020 0.002 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 4307) covalent geometry : angle 0.61483 / 0.32 ( 6017) hydrogen bonds : bond 0.05086 / 2.94 ( 153) hydrogen bonds : angle 5.20177 / 3.69 ( 399) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.079 Fit side-chains REVERT: A 446 ILE cc_start: 0.5142 (OUTLIER) cc_final: 0.4822 (tt) REVERT: A 505 PHE cc_start: 0.5849 (OUTLIER) cc_final: 0.4838 (t80) REVERT: A 542 MET cc_start: 0.5153 (pmm) cc_final: 0.4256 (ptp) REVERT: A 549 MET cc_start: 0.6492 (OUTLIER) cc_final: 0.6104 (ptm) REVERT: A 639 ILE cc_start: 0.4519 (OUTLIER) cc_final: 0.4040 (mm) REVERT: A 774 PHE cc_start: 0.5896 (OUTLIER) cc_final: 0.5523 (m-10) outliers start: 17 outliers final: 4 residues processed: 56 average time/residue: 0.4597 time to fit residues: 26.6827 Evaluate side-chains 49 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 774 PHE Chi-restraints excluded: chain A residue 839 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 43 optimal weight: 50.0000 chunk 32 optimal weight: 0.0470 chunk 1 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 17 optimal weight: 0.0040 overall best weight: 0.4690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 ASN A 548 GLN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5156 r_free = 0.5156 target = 0.286946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.246892 restraints weight = 4555.164| |-----------------------------------------------------------------------------| r_work (start): 0.4875 rms_B_bonded: 2.17 r_work: 0.4770 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5229 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4307 Z= 0.132 Angle : 0.600 7.304 6017 Z= 0.316 Chirality : 0.043 0.234 707 Planarity : 0.004 0.035 635 Dihedral : 20.681 153.465 1039 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.02 % Favored : 93.73 % Rotamer: Outliers : 4.99 % Allowed : 30.75 % Favored : 64.27 % 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 (0.42), residues: 415 helix: 0.57 (0.43), residues: 147 sheet: -1.22 (0.54), residues: 81 loop : -1.02 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 668 TYR 0.017 0.002 TYR A 784 PHE 0.013 0.001 PHE A 811 TRP 0.005 0.001 TRP A 769 HIS 0.016 0.002 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 4307) covalent geometry : angle 0.60027 / 0.32 ( 6017) hydrogen bonds : bond 0.04995 / 2.84 ( 153) hydrogen bonds : angle 5.08767 / 3.60 ( 399) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.077 Fit side-chains REVERT: A 446 ILE cc_start: 0.5156 (OUTLIER) cc_final: 0.4859 (tt) REVERT: A 505 PHE cc_start: 0.5430 (OUTLIER) cc_final: 0.4480 (t80) REVERT: A 542 MET cc_start: 0.5291 (pmm) cc_final: 0.4403 (ptp) REVERT: A 549 MET cc_start: 0.6465 (OUTLIER) cc_final: 0.6038 (ptm) REVERT: A 710 ARG cc_start: 0.4564 (tpt-90) cc_final: 0.2874 (tmt-80) REVERT: A 764 HIS cc_start: 0.3491 (m90) cc_final: 0.3237 (m90) REVERT: A 774 PHE cc_start: 0.5782 (OUTLIER) cc_final: 0.5432 (m-10) REVERT: A 789 THR cc_start: 0.6776 (OUTLIER) cc_final: 0.6567 (m) REVERT: A 839 HIS cc_start: 0.6321 (OUTLIER) cc_final: 0.5556 (p90) REVERT: A 853 LEU cc_start: 0.5270 (OUTLIER) cc_final: 0.4903 (mp) outliers start: 18 outliers final: 5 residues processed: 58 average time/residue: 0.4362 time to fit residues: 26.3098 Evaluate side-chains 50 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 774 PHE Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 853 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 50.0000 chunk 0 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 548 GLN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5156 r_free = 0.5156 target = 0.285101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.245985 restraints weight = 4456.938| |-----------------------------------------------------------------------------| r_work (start): 0.4847 rms_B_bonded: 1.97 r_work: 0.4711 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5418 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4307 Z= 0.149 Angle : 0.607 7.250 6017 Z= 0.320 Chirality : 0.043 0.234 707 Planarity : 0.005 0.037 635 Dihedral : 20.645 153.356 1039 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 4.43 % Allowed : 31.86 % Favored : 63.71 % 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: -0.77 (0.42), residues: 415 helix: 0.59 (0.43), residues: 147 sheet: -1.22 (0.55), residues: 81 loop : -0.99 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 423 TYR 0.013 0.002 TYR A 784 PHE 0.013 0.001 PHE A 811 TRP 0.005 0.001 TRP A 769 HIS 0.017 0.002 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 4307) covalent geometry : angle 0.60704 / 0.32 ( 6017) hydrogen bonds : bond 0.05219 / 2.93 ( 153) hydrogen bonds : angle 5.06803 / 3.58 ( 399) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.154 Fit side-chains REVERT: A 446 ILE cc_start: 0.5267 (OUTLIER) cc_final: 0.4930 (tt) REVERT: A 505 PHE cc_start: 0.5852 (OUTLIER) cc_final: 0.4770 (t80) REVERT: A 542 MET cc_start: 0.5129 (pmm) cc_final: 0.4442 (ptp) REVERT: A 549 MET cc_start: 0.6535 (OUTLIER) cc_final: 0.6149 (ptm) REVERT: A 774 PHE cc_start: 0.5932 (OUTLIER) cc_final: 0.5547 (m-10) REVERT: A 789 THR cc_start: 0.6525 (OUTLIER) cc_final: 0.6273 (m) outliers start: 16 outliers final: 4 residues processed: 55 average time/residue: 0.4808 time to fit residues: 27.5668 Evaluate side-chains 48 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 774 PHE Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 789 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 43 optimal weight: 50.0000 chunk 4 optimal weight: 0.2980 chunk 6 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 548 GLN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5152 r_free = 0.5152 target = 0.286637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.246840 restraints weight = 4569.979| |-----------------------------------------------------------------------------| r_work (start): 0.4874 rms_B_bonded: 2.17 r_work: 0.4772 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5258 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4307 Z= 0.141 Angle : 0.608 7.194 6017 Z= 0.322 Chirality : 0.043 0.234 707 Planarity : 0.004 0.036 635 Dihedral : 20.576 153.460 1039 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 4.71 % Allowed : 32.13 % Favored : 63.16 % 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: -0.70 (0.42), residues: 415 helix: 0.60 (0.43), residues: 148 sheet: -1.13 (0.55), residues: 80 loop : -0.94 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 814 TYR 0.026 0.002 TYR A 784 PHE 0.012 0.001 PHE A 811 TRP 0.005 0.001 TRP A 769 HIS 0.009 0.002 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 4307) covalent geometry : angle 0.60757 / 0.32 ( 6017) hydrogen bonds : bond 0.05150 / 2.91 ( 153) hydrogen bonds : angle 5.03034 / 3.54 ( 399) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.197 Fit side-chains REVERT: A 446 ILE cc_start: 0.5402 (OUTLIER) cc_final: 0.5088 (tt) REVERT: A 505 PHE cc_start: 0.5509 (OUTLIER) cc_final: 0.4548 (t80) REVERT: A 542 MET cc_start: 0.5418 (pmm) cc_final: 0.4704 (ptp) REVERT: A 549 MET cc_start: 0.6492 (OUTLIER) cc_final: 0.6035 (ptm) REVERT: A 697 ASP cc_start: 0.6026 (OUTLIER) cc_final: 0.5640 (m-30) REVERT: A 774 PHE cc_start: 0.5802 (OUTLIER) cc_final: 0.5443 (m-10) outliers start: 17 outliers final: 2 residues processed: 56 average time/residue: 0.4692 time to fit residues: 27.4576 Evaluate side-chains 47 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 774 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 25 optimal weight: 0.5980 chunk 32 optimal weight: 0.0000 chunk 28 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 548 GLN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5148 r_free = 0.5148 target = 0.286656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.247593 restraints weight = 4493.479| |-----------------------------------------------------------------------------| r_work (start): 0.4877 rms_B_bonded: 2.14 r_work: 0.4778 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5252 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4307 Z= 0.140 Angle : 0.621 7.647 6017 Z= 0.324 Chirality : 0.043 0.234 707 Planarity : 0.004 0.037 635 Dihedral : 20.533 153.429 1039 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.05 % Allowed : 33.52 % Favored : 63.43 % 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: -0.70 (0.42), residues: 415 helix: 0.65 (0.43), residues: 148 sheet: -1.23 (0.54), residues: 80 loop : -0.92 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 814 TYR 0.012 0.002 TYR A 804 PHE 0.012 0.001 PHE A 811 TRP 0.008 0.001 TRP A 435 HIS 0.007 0.002 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 4307) covalent geometry : angle 0.62107 / 0.32 ( 6017) hydrogen bonds : bond 0.05098 / 2.87 ( 153) hydrogen bonds : angle 5.03899 / 3.56 ( 399) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.078 Fit side-chains REVERT: A 437 MET cc_start: 0.4571 (ttp) cc_final: 0.3891 (tpt) REVERT: A 446 ILE cc_start: 0.5424 (OUTLIER) cc_final: 0.5088 (tt) REVERT: A 505 PHE cc_start: 0.5404 (OUTLIER) cc_final: 0.4401 (t80) REVERT: A 542 MET cc_start: 0.5443 (pmm) cc_final: 0.4675 (ptp) REVERT: A 549 MET cc_start: 0.6474 (OUTLIER) cc_final: 0.6024 (ptm) REVERT: A 668 ARG cc_start: 0.7074 (tpt170) cc_final: 0.6868 (tpt170) REVERT: A 774 PHE cc_start: 0.5774 (OUTLIER) cc_final: 0.5418 (m-10) REVERT: A 789 THR cc_start: 0.6667 (OUTLIER) cc_final: 0.6404 (m) outliers start: 11 outliers final: 2 residues processed: 51 average time/residue: 0.4066 time to fit residues: 21.6072 Evaluate side-chains 46 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 774 PHE Chi-restraints excluded: chain A residue 789 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 27 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 548 GLN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5151 r_free = 0.5151 target = 0.286581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.247210 restraints weight = 4516.215| |-----------------------------------------------------------------------------| r_work (start): 0.4877 rms_B_bonded: 2.14 r_work: 0.4774 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5269 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4307 Z= 0.143 Angle : 0.616 7.605 6017 Z= 0.324 Chirality : 0.044 0.234 707 Planarity : 0.004 0.037 635 Dihedral : 20.473 153.247 1039 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.60 % Allowed : 32.69 % Favored : 63.71 % 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: -0.64 (0.42), residues: 415 helix: 0.71 (0.44), residues: 148 sheet: -1.19 (0.54), residues: 80 loop : -0.90 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 814 TYR 0.031 0.002 TYR A 784 PHE 0.011 0.001 PHE A 811 TRP 0.007 0.001 TRP A 435 HIS 0.006 0.002 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 4307) covalent geometry : angle 0.61574 / 0.32 ( 6017) hydrogen bonds : bond 0.05186 / 2.91 ( 153) hydrogen bonds : angle 5.01666 / 3.53 ( 399) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1441.96 seconds wall clock time: 25 minutes 21.55 seconds (1521.55 seconds total)