Starting phenix.real_space_refine on Wed Jul 1 23:15:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6s_62134/07_2026/9k6s_62134.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6s_62134/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9k6s_62134/07_2026/9k6s_62134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6s_62134/07_2026/9k6s_62134.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k6s_62134/07_2026/9k6s_62134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6s_62134/07_2026/9k6s_62134.map" } 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-dev-6108/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: 1.16, per 1000 atoms: 0.28 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 129.7 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: 0.49 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: 0.64 Time building geometry restraints manager: 0.49 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=" N HIS A 634 " pdb=" CA HIS A 634 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.24e-02 6.50e+03 6.17e+00 ... (remaining 4302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 5694 1.85 - 3.69: 262 3.69 - 5.54: 29 5.54 - 7.39: 25 7.39 - 9.24: 7 Bond angle restraints: 6017 Sorted by residual: angle pdb=" O2' U B 12 " pdb=" C2' U B 12 " pdb=" C1' U B 12 " ideal model delta sigma weight residual 111.80 102.56 9.24 1.50e+00 4.44e-01 3.79e+01 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=" 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: 656 0.109 - 0.219: 40 0.219 - 0.328: 3 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: 0.260 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.220 Find NCS groups from input model: 0.010 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:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.110 ------------------------------------------------------------------------------- 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= 0.312 Angle : 0.944 9.236 6017 Z= 0.588 Chirality : 0.076 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 0.00511 / 0.31 ( 4307) covalent geometry : angle 0.94359 / 0.59 ( 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 : 0.163 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: 0.5882 time to fit residues: 41.9061 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 : 0.119 ------------------------------------------------------------------------------- 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 = 0.5211 r_free = 0.5211 target = 0.296586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.257781 restraints weight = 4639.253| |-----------------------------------------------------------------------------| r_work (start): 0.4930 rms_B_bonded: 2.19 r_work: 0.4830 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4940 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4307 Z= 0.137 Angle : 0.609 7.620 6017 Z= 0.328 Chirality : 0.043 0.200 707 Planarity : 0.005 0.064 635 Dihedral : 21.219 151.930 1047 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 5.82 % Allowed : 29.09 % Favored : 65.10 % 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: -1.18 (0.41), residues: 415 helix: 0.10 (0.42), residues: 144 sheet: -1.36 (0.56), residues: 79 loop : -1.11 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 0.00298 / 0.14 ( 4307) covalent geometry : angle 0.60877 / 0.33 ( 6017) hydrogen bonds : bond 0.05687 / 3.47 ( 153) hydrogen bonds : angle 5.78953 / 4.04 ( 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 69 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 490 CYS cc_start: 0.2746 (OUTLIER) cc_final: 0.1680 (p) REVERT: A 639 ILE cc_start: 0.4225 (OUTLIER) cc_final: 0.3802 (mt) REVERT: A 663 ARG cc_start: 0.5283 (mpt-90) cc_final: 0.4998 (mmm-85) REVERT: A 666 PHE cc_start: 0.4986 (t80) cc_final: 0.4401 (t80) REVERT: A 697 ASP cc_start: 0.5598 (OUTLIER) cc_final: 0.5078 (m-30) REVERT: A 710 ARG cc_start: 0.4313 (OUTLIER) cc_final: 0.2838 (tmt-80) outliers start: 21 outliers final: 4 residues processed: 64 average time/residue: 0.5054 time to fit residues: 33.5608 Evaluate side-chains 51 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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 569 VAL Chi-restraints excluded: chain A residue 639 ILE 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 19 optimal weight: 0.0020 chunk 34 optimal weight: 4.9990 chunk 2 optimal weight: 0.0030 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 ASN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 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 = 0.5207 r_free = 0.5207 target = 0.295853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.256675 restraints weight = 4644.957| |-----------------------------------------------------------------------------| r_work (start): 0.4918 rms_B_bonded: 2.21 r_work: 0.4816 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4983 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4307 Z= 0.123 Angle : 0.578 5.683 6017 Z= 0.314 Chirality : 0.043 0.205 707 Planarity : 0.005 0.034 635 Dihedral : 21.095 151.402 1043 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % 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: -0.99 (0.42), residues: 415 helix: 0.28 (0.43), residues: 144 sheet: -1.32 (0.55), residues: 79 loop : -1.00 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 814 TYR 0.012 0.002 TYR A 698 PHE 0.028 0.002 PHE A 811 TRP 0.006 0.001 TRP A 769 HIS 0.010 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 4307) covalent geometry : angle 0.57756 / 0.31 ( 6017) hydrogen bonds : bond 0.05169 / 3.03 ( 153) hydrogen bonds : angle 5.44311 / 3.83 ( 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 69 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 45 time to evaluate : 0.122 Fit side-chains REVERT: A 490 CYS cc_start: 0.2765 (OUTLIER) cc_final: 0.1737 (p) REVERT: A 663 ARG cc_start: 0.5330 (mpt-90) cc_final: 0.4992 (mmm-85) REVERT: A 666 PHE cc_start: 0.5119 (t80) cc_final: 0.4505 (t80) outliers start: 24 outliers final: 4 residues processed: 62 average time/residue: 0.4073 time to fit residues: 26.2479 Evaluate side-chains 45 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.108 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 0.0770 chunk 39 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 ** 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 = 0.5191 r_free = 0.5191 target = 0.294054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.255070 restraints weight = 4620.076| |-----------------------------------------------------------------------------| r_work (start): 0.4905 rms_B_bonded: 2.18 r_work: 0.4806 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5030 moved from start: 0.2572 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= 0.130 Angle : 0.584 5.409 6017 Z= 0.314 Chirality : 0.044 0.255 707 Planarity : 0.004 0.032 635 Dihedral : 20.951 151.135 1039 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 5.54 % Allowed : 29.09 % 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: -0.93 (0.42), residues: 415 helix: 0.27 (0.43), residues: 147 sheet: -1.21 (0.56), residues: 79 loop : -0.96 (0.48), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 814 TYR 0.011 0.002 TYR A 784 PHE 0.013 0.001 PHE A 811 TRP 0.005 0.001 TRP A 769 HIS 0.007 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 4307) covalent geometry : angle 0.58429 / 0.31 ( 6017) hydrogen bonds : bond 0.05123 / 3.00 ( 153) hydrogen bonds : angle 5.31863 / 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 62 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.123 Fit side-chains REVERT: A 490 CYS cc_start: 0.3015 (OUTLIER) cc_final: 0.2036 (p) REVERT: A 505 PHE cc_start: 0.4986 (OUTLIER) cc_final: 0.4183 (t80) REVERT: A 549 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.6239 (ptm) REVERT: A 639 ILE cc_start: 0.4288 (OUTLIER) cc_final: 0.3951 (mm) REVERT: A 663 ARG cc_start: 0.5140 (mpt-90) cc_final: 0.4748 (mmm-85) REVERT: A 666 PHE cc_start: 0.5221 (t80) cc_final: 0.4750 (t80) REVERT: A 689 GLU cc_start: 0.5142 (OUTLIER) cc_final: 0.4688 (tm-30) outliers start: 20 outliers final: 2 residues processed: 57 average time/residue: 0.3947 time to fit residues: 23.4641 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 : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 490 CYS 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 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: 1.9990 chunk 19 optimal weight: 0.0570 chunk 43 optimal weight: 30.0000 chunk 10 optimal weight: 0.0570 chunk 8 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 overall best weight: 0.5220 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5207 r_free = 0.5207 target = 0.293515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.256899 restraints weight = 4589.580| |-----------------------------------------------------------------------------| r_work (start): 0.4932 rms_B_bonded: 2.06 r_work: 0.4829 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5072 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4307 Z= 0.121 Angle : 0.570 6.068 6017 Z= 0.306 Chirality : 0.044 0.207 707 Planarity : 0.004 0.031 635 Dihedral : 20.845 151.292 1039 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 6.37 % Allowed : 29.09 % 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: -0.83 (0.42), residues: 415 helix: 0.43 (0.44), residues: 146 sheet: -1.17 (0.56), residues: 79 loop : -0.96 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 710 TYR 0.011 0.002 TYR A 857 PHE 0.020 0.002 PHE A 811 TRP 0.004 0.001 TRP A 769 HIS 0.007 0.001 HIS A 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 4307) covalent geometry : angle 0.56973 / 0.31 ( 6017) hydrogen bonds : bond 0.04916 / 2.82 ( 153) hydrogen bonds : angle 5.25088 / 3.74 ( 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 64 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 41 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: A 490 CYS cc_start: 0.3037 (OUTLIER) cc_final: 0.2114 (p) REVERT: A 505 PHE cc_start: 0.5040 (OUTLIER) cc_final: 0.4162 (t80) REVERT: A 549 MET cc_start: 0.6698 (OUTLIER) cc_final: 0.6247 (ptm) REVERT: A 663 ARG cc_start: 0.5187 (mpt-90) cc_final: 0.4764 (mmm-85) REVERT: A 666 PHE cc_start: 0.5315 (t80) cc_final: 0.4880 (t80) REVERT: A 689 GLU cc_start: 0.5530 (OUTLIER) cc_final: 0.5124 (tm-30) outliers start: 23 outliers final: 5 residues processed: 59 average time/residue: 0.3483 time to fit residues: 21.4778 Evaluate side-chains 47 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.126 ------------------------------------------------------------------------------- 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 505 PHE Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 811 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 516 GLN A 548 GLN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN A 600 HIS ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5146 r_free = 0.5146 target = 0.285641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.246139 restraints weight = 4606.552| |-----------------------------------------------------------------------------| r_work (start): 0.4820 rms_B_bonded: 2.13 r_work: 0.4718 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5276 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4307 Z= 0.189 Angle : 0.659 6.951 6017 Z= 0.352 Chirality : 0.047 0.204 707 Planarity : 0.005 0.038 635 Dihedral : 20.858 150.526 1039 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.78 % Favored : 93.98 % Rotamer: Outliers : 6.65 % Allowed : 29.09 % 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: -0.98 (0.42), residues: 415 helix: 0.28 (0.43), residues: 146 sheet: -1.20 (0.54), residues: 81 loop : -1.04 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 814 TYR 0.027 0.003 TYR A 804 PHE 0.028 0.002 PHE A 811 TRP 0.006 0.001 TRP A 769 HIS 0.006 0.002 HIS A 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 ( 4307) covalent geometry : angle 0.65916 / 0.35 ( 6017) hydrogen bonds : bond 0.05863 / 3.27 ( 153) hydrogen bonds : angle 5.25165 / 3.76 ( 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 64 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 40 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: A 490 CYS cc_start: 0.3473 (OUTLIER) cc_final: 0.2480 (p) REVERT: A 505 PHE cc_start: 0.5259 (OUTLIER) cc_final: 0.4314 (t80) REVERT: A 542 MET cc_start: 0.5155 (pmm) cc_final: 0.4208 (ptp) REVERT: A 549 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.6344 (ptm) REVERT: A 639 ILE cc_start: 0.4432 (OUTLIER) cc_final: 0.3970 (mm) REVERT: A 702 ILE cc_start: 0.5174 (OUTLIER) cc_final: 0.4697 (mt) REVERT: A 709 LYS cc_start: 0.6028 (OUTLIER) cc_final: 0.5740 (mttt) REVERT: A 807 HIS cc_start: 0.6220 (t-90) cc_final: 0.6009 (t-170) outliers start: 24 outliers final: 6 residues processed: 59 average time/residue: 0.4012 time to fit residues: 24.5120 Evaluate side-chains 51 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.076 ------------------------------------------------------------------------------- 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 505 PHE Chi-restraints excluded: chain A residue 549 MET 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 709 LYS Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 811 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: 0.8980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 43 optimal weight: 30.0000 chunk 32 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 17 optimal weight: 0.0030 overall best weight: 0.6590 ------------------------------------------------------------------------------- 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 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 GLN ** 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 = 0.5163 r_free = 0.5163 target = 0.286454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.247693 restraints weight = 4496.962| |-----------------------------------------------------------------------------| r_work (start): 0.4856 rms_B_bonded: 1.95 r_work: 0.4719 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5385 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4307 Z= 0.141 Angle : 0.604 6.640 6017 Z= 0.323 Chirality : 0.044 0.206 707 Planarity : 0.004 0.035 635 Dihedral : 20.801 151.451 1039 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.16 % Allowed : 32.13 % 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: -0.85 (0.42), residues: 415 helix: 0.51 (0.43), residues: 147 sheet: -1.22 (0.54), residues: 81 loop : -1.03 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 814 TYR 0.013 0.002 TYR A 784 PHE 0.022 0.002 PHE A 811 TRP 0.005 0.001 TRP A 769 HIS 0.016 0.002 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 4307) covalent geometry : angle 0.60398 / 0.32 ( 6017) hydrogen bonds : bond 0.05195 / 2.93 ( 153) hydrogen bonds : angle 5.16235 / 3.70 ( 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 54 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.089 Fit side-chains revert: symmetry clash REVERT: A 505 PHE cc_start: 0.5587 (OUTLIER) cc_final: 0.4553 (t80) REVERT: A 542 MET cc_start: 0.5175 (pmm) cc_final: 0.4286 (ptp) REVERT: A 549 MET cc_start: 0.6466 (OUTLIER) cc_final: 0.6092 (ptm) REVERT: A 554 ARG cc_start: 0.6530 (mpp-170) cc_final: 0.6199 (mtm-85) REVERT: A 639 ILE cc_start: 0.4445 (OUTLIER) cc_final: 0.3960 (mm) REVERT: A 839 HIS cc_start: 0.6297 (OUTLIER) cc_final: 0.5526 (p90) outliers start: 15 outliers final: 4 residues processed: 52 average time/residue: 0.4604 time to fit residues: 24.9158 Evaluate side-chains 46 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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 639 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 839 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 10 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 43 optimal weight: 40.0000 chunk 0 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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 772 ASN ** A 785 GLN ** 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 = 0.5115 r_free = 0.5115 target = 0.281761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.240043 restraints weight = 4462.579| |-----------------------------------------------------------------------------| r_work (start): 0.4830 rms_B_bonded: 2.18 r_work: 0.4728 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5348 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4307 Z= 0.196 Angle : 0.653 6.411 6017 Z= 0.349 Chirality : 0.046 0.205 707 Planarity : 0.005 0.042 635 Dihedral : 20.821 151.244 1039 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.23 % Favored : 92.53 % Rotamer: Outliers : 4.99 % Allowed : 32.13 % Favored : 62.88 % 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: -0.97 (0.42), residues: 415 helix: 0.32 (0.43), residues: 148 sheet: -1.19 (0.53), residues: 82 loop : -1.09 (0.48), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 814 TYR 0.019 0.003 TYR A 784 PHE 0.021 0.002 PHE A 811 TRP 0.005 0.001 TRP A 769 HIS 0.032 0.003 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 ( 4307) covalent geometry : angle 0.65305 / 0.35 ( 6017) hydrogen bonds : bond 0.05832 / 3.22 ( 153) hydrogen bonds : angle 5.19221 / 3.70 ( 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: 18 poor density : 39 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 505 PHE cc_start: 0.5268 (OUTLIER) cc_final: 0.4250 (t80) REVERT: A 542 MET cc_start: 0.5496 (pmm) cc_final: 0.4621 (ptp) REVERT: A 548 GLN cc_start: 0.5623 (OUTLIER) cc_final: 0.5292 (tt0) REVERT: A 549 MET cc_start: 0.6546 (OUTLIER) cc_final: 0.6057 (ptm) REVERT: A 639 ILE cc_start: 0.4444 (OUTLIER) cc_final: 0.3888 (mm) outliers start: 18 outliers final: 6 residues processed: 55 average time/residue: 0.4947 time to fit residues: 28.3836 Evaluate side-chains 45 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 555 THR 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 781 ILE Chi-restraints excluded: chain A residue 811 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 0.0970 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 31 optimal weight: 7.9990 chunk 43 optimal weight: 30.0000 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 839 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5146 r_free = 0.5146 target = 0.286180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.246561 restraints weight = 4573.032| |-----------------------------------------------------------------------------| r_work (start): 0.4858 rms_B_bonded: 2.14 r_work: 0.4757 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5268 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4307 Z= 0.146 Angle : 0.623 7.553 6017 Z= 0.333 Chirality : 0.045 0.204 707 Planarity : 0.005 0.040 635 Dihedral : 20.788 151.817 1039 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 4.16 % Allowed : 33.52 % Favored : 62.33 % 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: -0.90 (0.41), residues: 415 helix: 0.48 (0.43), residues: 148 sheet: -1.28 (0.53), residues: 81 loop : -1.08 (0.48), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 814 TYR 0.020 0.002 TYR A 784 PHE 0.017 0.002 PHE A 811 TRP 0.004 0.001 TRP A 769 HIS 0.006 0.001 HIS A 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 4307) covalent geometry : angle 0.62268 / 0.33 ( 6017) hydrogen bonds : bond 0.05277 / 2.98 ( 153) hydrogen bonds : angle 5.13986 / 3.66 ( 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 54 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.130 Fit side-chains revert: symmetry clash REVERT: A 505 PHE cc_start: 0.5285 (OUTLIER) cc_final: 0.4216 (t80) REVERT: A 542 MET cc_start: 0.5337 (pmm) cc_final: 0.4518 (ptp) REVERT: A 548 GLN cc_start: 0.5548 (OUTLIER) cc_final: 0.5126 (tt0) REVERT: A 549 MET cc_start: 0.6539 (OUTLIER) cc_final: 0.6196 (ptm) REVERT: A 774 PHE cc_start: 0.5768 (OUTLIER) cc_final: 0.5413 (m-10) outliers start: 15 outliers final: 5 residues processed: 52 average time/residue: 0.4557 time to fit residues: 24.7579 Evaluate side-chains 47 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 555 THR 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 811 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 22 optimal weight: 0.2980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 807 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 = 0.5142 r_free = 0.5142 target = 0.285933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.246687 restraints weight = 4464.630| |-----------------------------------------------------------------------------| r_work (start): 0.4819 rms_B_bonded: 2.11 r_work: 0.4718 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5248 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4307 Z= 0.147 Angle : 0.621 7.646 6017 Z= 0.333 Chirality : 0.045 0.204 707 Planarity : 0.004 0.038 635 Dihedral : 20.762 152.128 1039 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.32 % Allowed : 34.35 % Favored : 62.33 % 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: 0.73 (0.44), residues: 142 sheet: -1.40 (0.49), residues: 90 loop : -0.92 (0.49), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 814 TYR 0.014 0.002 TYR A 804 PHE 0.024 0.002 PHE A 811 TRP 0.004 0.001 TRP A 769 HIS 0.006 0.001 HIS A 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 4307) covalent geometry : angle 0.62063 / 0.33 ( 6017) hydrogen bonds : bond 0.05225 / 2.94 ( 153) hydrogen bonds : angle 5.12750 / 3.64 ( 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 50 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 437 MET cc_start: 0.4608 (ttp) cc_final: 0.3900 (tpt) REVERT: A 505 PHE cc_start: 0.5268 (OUTLIER) cc_final: 0.4201 (t80) REVERT: A 542 MET cc_start: 0.5333 (pmm) cc_final: 0.4587 (ptp) REVERT: A 549 MET cc_start: 0.6622 (OUTLIER) cc_final: 0.6147 (ptm) REVERT: A 774 PHE cc_start: 0.5771 (OUTLIER) cc_final: 0.5430 (m-10) REVERT: A 853 LEU cc_start: 0.5317 (OUTLIER) cc_final: 0.4946 (mp) outliers start: 12 outliers final: 5 residues processed: 49 average time/residue: 0.4960 time to fit residues: 25.3024 Evaluate side-chains 46 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 GLN 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 736 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 774 PHE Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 853 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5147 r_free = 0.5147 target = 0.286181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.247135 restraints weight = 4508.545| |-----------------------------------------------------------------------------| r_work (start): 0.4863 rms_B_bonded: 2.10 r_work: 0.4764 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5267 moved from start: 0.4074 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= 0.146 Angle : 0.634 8.625 6017 Z= 0.338 Chirality : 0.045 0.204 707 Planarity : 0.004 0.039 635 Dihedral : 20.743 152.556 1039 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.05 % Allowed : 34.63 % Favored : 62.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.42), residues: 415 helix: 0.55 (0.44), residues: 148 sheet: -1.36 (0.48), residues: 89 loop : -0.97 (0.50), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 814 TYR 0.020 0.002 TYR A 784 PHE 0.010 0.001 PHE A 811 TRP 0.004 0.001 TRP A 769 HIS 0.006 0.001 HIS A 764 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 4307) covalent geometry : angle 0.63435 / 0.34 ( 6017) hydrogen bonds : bond 0.05175 / 2.88 ( 153) hydrogen bonds : angle 5.05889 / 3.61 ( 399) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1421.81 seconds wall clock time: 25 minutes 1.17 seconds (1501.17 seconds total)