Starting phenix.real_space_refine on Wed Sep 17 06:32:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6q_62132/09_2025/9k6q_62132.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6q_62132/09_2025/9k6q_62132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k6q_62132/09_2025/9k6q_62132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6q_62132/09_2025/9k6q_62132.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k6q_62132/09_2025/9k6q_62132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6q_62132/09_2025/9k6q_62132.map" } resolution = 2.7 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= 0.054 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 31 5.49 5 Mg 1 5.21 5 S 35 5.16 5 C 3867 2.51 5 N 1123 2.21 5 O 1219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6276 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 358 Classifications: {'RNA': 17} Modifications used: {'p5*END': 1, 'rna2p_pyr': 3, 'rna3p_pur': 7, 'rna3p_pyr': 7} Link IDs: {'rna2p': 2, 'rna3p': 14} Chain: "C" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 298 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna2p': 4, 'rna3p': 9} Chain: "A" Number of atoms: 5619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5619 Classifications: {'peptide': 706} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 660} Chain breaks: 2 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: 1.79, per 1000 atoms: 0.29 Number of scatterers: 6276 At special positions: 0 Unit cell: (74.1, 76.38, 108.3, 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 35 16.00 P 31 15.00 Mg 1 11.99 O 1219 8.00 N 1123 7.00 C 3867 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: 0.49 Conformation dependent library (CDL) restraints added in 348.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1324 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 5 sheets defined 36.0% alpha, 20.0% beta 9 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.564A pdb=" N SER A 148 " --> pdb=" O HIS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 168 Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 358 through 369 removed outlier: 3.610A pdb=" N SER A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 387 Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 391 through 396 Processing helix chain 'A' and resid 463 through 481 Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 512 Processing helix chain 'A' and resid 526 through 538 removed outlier: 4.279A pdb=" N ALA A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 556 through 571 Processing helix chain 'A' and resid 580 through 583 removed outlier: 3.896A pdb=" N ARG A 583 " --> pdb=" O PRO A 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 583' Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.530A pdb=" N GLN A 589 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 658 Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 675 through 695 removed outlier: 3.635A pdb=" N LEU A 685 " --> pdb=" O HIS A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 723 Processing helix chain 'A' and resid 775 through 788 Processing helix chain 'A' and resid 800 through 817 Processing helix chain 'A' and resid 839 through 844 Processing helix chain 'A' and resid 849 through 854 removed outlier: 4.452A pdb=" N ARG A 854 " --> pdb=" O GLN A 850 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 625 through 632 removed outlier: 5.065A pdb=" N PHE A 593 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL A 598 " --> pdb=" O ALA A 669 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE A 702 " --> pdb=" O ASP A 770 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP A 770 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE A 704 " --> pdb=" O LEU A 768 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 734 " --> pdb=" O CYS A 751 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 175 through 177 removed outlier: 4.168A pdb=" N MET A 213 " --> pdb=" O MET A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 94 removed outlier: 7.009A pdb=" N ILE A 54 " --> pdb=" O CYS A 137 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N CYS A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N HIS A 56 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS A 129 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 132 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A 113 " --> pdb=" O ILE A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 427 through 428 Processing sheet with id=AA5, first strand: chain 'A' and resid 491 through 494 removed outlier: 3.976A pdb=" N PHE A 491 " --> pdb=" O TRP A 451 " (cutoff:3.500A) 262 hydrogen bonds defined for protein. 741 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1698 1.33 - 1.45: 1259 1.45 - 1.57: 3414 1.57 - 1.69: 60 1.69 - 1.81: 54 Bond restraints: 6485 Sorted by residual: bond pdb=" P A C 4 " pdb=" O5' A C 4 " ideal model delta sigma weight residual 1.593 1.634 -0.041 1.50e-02 4.44e+03 7.33e+00 bond pdb=" O5' A C 4 " pdb=" C5' A C 4 " ideal model delta sigma weight residual 1.424 1.460 -0.036 1.50e-02 4.44e+03 5.85e+00 bond pdb=" N LYS A 355 " pdb=" CA LYS A 355 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.19e-02 7.06e+03 5.83e+00 bond pdb=" N GLN A 757 " pdb=" CA GLN A 757 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.25e-02 6.40e+03 5.82e+00 bond pdb=" O5' G C 5 " pdb=" C5' G C 5 " ideal model delta sigma weight residual 1.420 1.456 -0.036 1.50e-02 4.44e+03 5.79e+00 ... (remaining 6480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 8818 3.12 - 6.24: 91 6.24 - 9.36: 14 9.36 - 12.48: 1 12.48 - 15.60: 2 Bond angle restraints: 8926 Sorted by residual: angle pdb=" O3' A C 4 " pdb=" C3' A C 4 " pdb=" C2' A C 4 " ideal model delta sigma weight residual 109.50 96.31 13.19 1.50e+00 4.44e-01 7.73e+01 angle pdb=" C3' A C 4 " pdb=" C2' A C 4 " pdb=" C1' A C 4 " ideal model delta sigma weight residual 101.50 95.33 6.17 1.00e+00 1.00e+00 3.80e+01 angle pdb=" C LYS A 709 " pdb=" CA LYS A 709 " pdb=" CB LYS A 709 " ideal model delta sigma weight residual 109.55 119.54 -9.99 1.68e+00 3.54e-01 3.54e+01 angle pdb=" N LYS A 709 " pdb=" CA LYS A 709 " pdb=" C LYS A 709 " ideal model delta sigma weight residual 113.72 106.12 7.60 1.30e+00 5.92e-01 3.42e+01 angle pdb=" O3' A C 4 " pdb=" P G C 5 " pdb=" OP2 G C 5 " ideal model delta sigma weight residual 108.00 123.60 -15.60 3.00e+00 1.11e-01 2.70e+01 ... (remaining 8921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 3741 35.05 - 70.10: 203 70.10 - 105.15: 20 105.15 - 140.20: 1 140.20 - 175.25: 2 Dihedral angle restraints: 3967 sinusoidal: 1917 harmonic: 2050 Sorted by residual: dihedral pdb=" CA HIS A 621 " pdb=" C HIS A 621 " pdb=" N PRO A 622 " pdb=" CA PRO A 622 " ideal model delta harmonic sigma weight residual -180.00 -113.10 -66.90 0 5.00e+00 4.00e-02 1.79e+02 dihedral pdb=" O4' U B 17 " pdb=" C1' U B 17 " pdb=" N1 U B 17 " pdb=" C2 U B 17 " ideal model delta sinusoidal sigma weight residual -128.00 47.25 -175.25 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U C 14 " pdb=" C1' U C 14 " pdb=" N1 U C 14 " pdb=" C2 U C 14 " ideal model delta sinusoidal sigma weight residual 232.00 58.90 173.10 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 3964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 961 0.116 - 0.231: 41 0.231 - 0.347: 1 0.347 - 0.462: 5 0.462 - 0.578: 4 Chirality restraints: 1012 Sorted by residual: chirality pdb=" P A C 4 " pdb=" OP1 A C 4 " pdb=" OP2 A C 4 " pdb=" O5' A C 4 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.34e+00 chirality pdb=" P U C 13 " pdb=" OP1 U C 13 " pdb=" OP2 U C 13 " pdb=" O5' U C 13 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 6.94e+00 chirality pdb=" P U C 14 " pdb=" OP1 U C 14 " pdb=" OP2 U C 14 " pdb=" O5' U C 14 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.80e+00 ... (remaining 1009 not shown) Planarity restraints: 1041 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 175 " 0.073 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO A 176 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 621 " 0.065 5.00e-02 4.00e+02 9.98e-02 1.59e+01 pdb=" N PRO A 622 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO A 622 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 622 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U B 13 " -0.034 2.00e-02 2.50e+03 1.88e-02 7.93e+00 pdb=" N1 U B 13 " 0.043 2.00e-02 2.50e+03 pdb=" C2 U B 13 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U B 13 " 0.004 2.00e-02 2.50e+03 pdb=" N3 U B 13 " -0.005 2.00e-02 2.50e+03 pdb=" C4 U B 13 " -0.004 2.00e-02 2.50e+03 pdb=" O4 U B 13 " -0.008 2.00e-02 2.50e+03 pdb=" C5 U B 13 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U B 13 " 0.003 2.00e-02 2.50e+03 ... (remaining 1038 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 928 2.76 - 3.30: 5633 3.30 - 3.83: 11560 3.83 - 4.37: 13361 4.37 - 4.90: 21958 Nonbonded interactions: 53440 Sorted by model distance: nonbonded pdb=" O HIS A 507 " pdb=" OG1 THR A 511 " model vdw 2.228 3.040 nonbonded pdb=" O GLN A 496 " pdb=" OG SER A 500 " model vdw 2.291 3.040 nonbonded pdb=" OG SER A 209 " pdb=" O LYS A 212 " model vdw 2.319 3.040 nonbonded pdb=" O LEU A 786 " pdb=" OG1 THR A 789 " model vdw 2.325 3.040 nonbonded pdb=" OG SER A 752 " pdb=" O VAL A 797 " model vdw 2.340 3.040 ... (remaining 53435 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.830 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 : 0.004 0.072 6485 Z= 0.217 Angle : 0.826 15.601 8926 Z= 0.459 Chirality : 0.068 0.578 1012 Planarity : 0.008 0.108 1041 Dihedral : 20.247 175.246 2643 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.00 % Favored : 95.86 % Rotamer: Outliers : 0.81 % Allowed : 21.17 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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 aren not related in a simple way. whole: -0.54 (0.31), residues: 700 helix: 0.52 (0.34), residues: 223 sheet: -0.23 (0.39), residues: 174 loop : -1.01 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 658 TYR 0.024 0.002 TYR A 55 PHE 0.013 0.002 PHE A 491 TRP 0.009 0.002 TRP A 199 HIS 0.006 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 6485) covalent geometry : angle 0.82552 ( 8926) hydrogen bonds : bond 0.16733 ( 284) hydrogen bonds : angle 7.63781 ( 781) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.241 Fit side-chains REVERT: A 637 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6467 (tp30) outliers start: 5 outliers final: 1 residues processed: 81 average time/residue: 0.8580 time to fit residues: 71.9011 Evaluate side-chains 65 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.0470 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.186780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.135738 restraints weight = 5950.037| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.35 r_work: 0.3301 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6485 Z= 0.140 Angle : 0.616 7.368 8926 Z= 0.329 Chirality : 0.046 0.289 1012 Planarity : 0.007 0.096 1041 Dihedral : 18.286 177.212 1253 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.86 % Favored : 96.00 % Rotamer: Outliers : 2.28 % Allowed : 22.96 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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 aren not related in a simple way. whole: -0.16 (0.32), residues: 700 helix: 1.16 (0.35), residues: 222 sheet: -0.42 (0.38), residues: 184 loop : -0.79 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 179 TYR 0.017 0.001 TYR A 55 PHE 0.010 0.001 PHE A 491 TRP 0.008 0.001 TRP A 435 HIS 0.007 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 6485) covalent geometry : angle 0.61582 ( 8926) hydrogen bonds : bond 0.04709 ( 284) hydrogen bonds : angle 5.44922 ( 781) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.257 Fit side-chains REVERT: A 473 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7708 (mp10) REVERT: A 637 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6987 (tp30) outliers start: 14 outliers final: 6 residues processed: 86 average time/residue: 0.7683 time to fit residues: 68.5400 Evaluate side-chains 79 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 756 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 13 optimal weight: 0.0070 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS A 507 HIS A 623 ASN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.188883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.141550 restraints weight = 5914.930| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.79 r_work: 0.3340 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6485 Z= 0.117 Angle : 0.579 7.356 8926 Z= 0.305 Chirality : 0.044 0.200 1012 Planarity : 0.006 0.094 1041 Dihedral : 18.163 179.851 1251 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.29 % Favored : 96.57 % Rotamer: Outliers : 2.77 % Allowed : 22.31 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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 aren not related in a simple way. whole: 0.05 (0.32), residues: 700 helix: 1.41 (0.35), residues: 224 sheet: -0.21 (0.39), residues: 182 loop : -0.82 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 179 TYR 0.019 0.001 TYR A 55 PHE 0.013 0.001 PHE A 491 TRP 0.008 0.001 TRP A 435 HIS 0.005 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6485) covalent geometry : angle 0.57856 ( 8926) hydrogen bonds : bond 0.04213 ( 284) hydrogen bonds : angle 5.10199 ( 781) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.258 Fit side-chains REVERT: A 133 LYS cc_start: 0.6214 (tppt) cc_final: 0.5855 (tppt) REVERT: A 405 MET cc_start: 0.8814 (mtt) cc_final: 0.8488 (mtt) REVERT: A 588 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8233 (mp10) REVERT: A 637 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6871 (tp30) outliers start: 17 outliers final: 6 residues processed: 80 average time/residue: 0.7859 time to fit residues: 65.3371 Evaluate side-chains 73 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 591 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 56 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 34 optimal weight: 0.0570 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.187806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.136938 restraints weight = 5916.212| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.34 r_work: 0.3303 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6485 Z= 0.128 Angle : 0.581 7.383 8926 Z= 0.305 Chirality : 0.044 0.204 1012 Planarity : 0.006 0.095 1041 Dihedral : 18.049 179.028 1251 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.86 % Favored : 96.00 % Rotamer: Outliers : 3.09 % Allowed : 22.15 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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 aren not related in a simple way. whole: 0.07 (0.32), residues: 700 helix: 1.54 (0.36), residues: 222 sheet: -0.25 (0.39), residues: 182 loop : -0.86 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 179 TYR 0.018 0.001 TYR A 55 PHE 0.013 0.001 PHE A 491 TRP 0.007 0.001 TRP A 435 HIS 0.003 0.001 HIS A 600 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6485) covalent geometry : angle 0.58118 ( 8926) hydrogen bonds : bond 0.04255 ( 284) hydrogen bonds : angle 5.00624 ( 781) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.202 Fit side-chains REVERT: A 73 GLU cc_start: 0.5690 (OUTLIER) cc_final: 0.5449 (tm-30) REVERT: A 133 LYS cc_start: 0.6220 (tppt) cc_final: 0.5830 (tppt) REVERT: A 472 GLU cc_start: 0.7657 (pt0) cc_final: 0.7454 (pt0) REVERT: A 473 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7739 (mp10) REVERT: A 637 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6913 (tp30) outliers start: 19 outliers final: 8 residues processed: 84 average time/residue: 0.7710 time to fit residues: 67.2139 Evaluate side-chains 79 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 756 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 GLN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 847 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.183239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.135506 restraints weight = 5969.141| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.32 r_work: 0.3266 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6485 Z= 0.192 Angle : 0.650 7.068 8926 Z= 0.340 Chirality : 0.047 0.237 1012 Planarity : 0.006 0.099 1041 Dihedral : 18.039 176.971 1251 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.56 % Allowed : 20.52 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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 aren not related in a simple way. whole: -0.03 (0.32), residues: 700 helix: 1.48 (0.36), residues: 221 sheet: -0.34 (0.39), residues: 182 loop : -0.91 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 375 TYR 0.021 0.002 TYR A 55 PHE 0.016 0.002 PHE A 491 TRP 0.010 0.002 TRP A 199 HIS 0.004 0.001 HIS A 849 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 6485) covalent geometry : angle 0.64971 ( 8926) hydrogen bonds : bond 0.04861 ( 284) hydrogen bonds : angle 5.24261 ( 781) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 0.243 Fit side-chains REVERT: A 73 GLU cc_start: 0.5927 (OUTLIER) cc_final: 0.5686 (tm-30) REVERT: A 133 LYS cc_start: 0.6220 (tppt) cc_final: 0.5813 (tppt) REVERT: A 472 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7454 (pt0) REVERT: A 473 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7710 (mp10) REVERT: A 517 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9010 (tp) REVERT: A 641 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7553 (t70) outliers start: 28 outliers final: 10 residues processed: 85 average time/residue: 0.7636 time to fit residues: 67.4992 Evaluate side-chains 81 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 818 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 17 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 13 optimal weight: 6.9990 chunk 47 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 GLN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.185320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.137507 restraints weight = 5916.298| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.29 r_work: 0.3294 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6485 Z= 0.144 Angle : 0.601 7.407 8926 Z= 0.314 Chirality : 0.045 0.220 1012 Planarity : 0.006 0.097 1041 Dihedral : 18.034 178.078 1251 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.93 % Allowed : 22.15 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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 aren not related in a simple way. whole: -0.03 (0.32), residues: 700 helix: 1.49 (0.36), residues: 222 sheet: -0.32 (0.38), residues: 181 loop : -0.94 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 97 TYR 0.021 0.001 TYR A 55 PHE 0.014 0.002 PHE A 491 TRP 0.008 0.001 TRP A 435 HIS 0.004 0.001 HIS A 712 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6485) covalent geometry : angle 0.60107 ( 8926) hydrogen bonds : bond 0.04325 ( 284) hydrogen bonds : angle 5.08804 ( 781) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.238 Fit side-chains REVERT: A 73 GLU cc_start: 0.5960 (OUTLIER) cc_final: 0.5729 (tm-30) REVERT: A 133 LYS cc_start: 0.6218 (tppt) cc_final: 0.5803 (tppt) REVERT: A 472 GLU cc_start: 0.7644 (pt0) cc_final: 0.7423 (pt0) REVERT: A 473 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7656 (mp10) REVERT: A 517 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9000 (tp) REVERT: A 637 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7000 (tp30) REVERT: A 641 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7556 (t0) outliers start: 18 outliers final: 10 residues processed: 85 average time/residue: 0.7758 time to fit residues: 68.5187 Evaluate side-chains 85 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 756 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 GLN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.184869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.136848 restraints weight = 5871.892| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.32 r_work: 0.3294 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6485 Z= 0.158 Angle : 0.614 7.303 8926 Z= 0.321 Chirality : 0.046 0.225 1012 Planarity : 0.006 0.097 1041 Dihedral : 18.075 177.515 1251 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.07 % Allowed : 21.66 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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 aren not related in a simple way. whole: -0.05 (0.32), residues: 700 helix: 1.51 (0.36), residues: 221 sheet: -0.31 (0.39), residues: 176 loop : -0.98 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.022 0.001 TYR A 55 PHE 0.015 0.002 PHE A 491 TRP 0.008 0.001 TRP A 435 HIS 0.004 0.001 HIS A 849 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 6485) covalent geometry : angle 0.61399 ( 8926) hydrogen bonds : bond 0.04518 ( 284) hydrogen bonds : angle 5.10679 ( 781) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.196 Fit side-chains REVERT: A 73 GLU cc_start: 0.5909 (OUTLIER) cc_final: 0.5667 (tm-30) REVERT: A 133 LYS cc_start: 0.6213 (tppt) cc_final: 0.5804 (tppt) REVERT: A 172 MET cc_start: 0.4996 (OUTLIER) cc_final: 0.4588 (ttm) REVERT: A 472 GLU cc_start: 0.7653 (pt0) cc_final: 0.7429 (pt0) REVERT: A 473 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7679 (mp10) REVERT: A 517 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9010 (tp) REVERT: A 637 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7025 (tp30) REVERT: A 641 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7565 (t70) outliers start: 25 outliers final: 12 residues processed: 87 average time/residue: 0.7931 time to fit residues: 71.5843 Evaluate side-chains 87 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 818 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 65 optimal weight: 0.0370 chunk 59 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 8 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 GLN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.188810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.137198 restraints weight = 5903.989| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.38 r_work: 0.3326 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6485 Z= 0.117 Angle : 0.575 7.577 8926 Z= 0.299 Chirality : 0.044 0.196 1012 Planarity : 0.006 0.095 1041 Dihedral : 18.018 179.407 1251 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.42 % Allowed : 22.15 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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 aren not related in a simple way. whole: 0.02 (0.32), residues: 700 helix: 1.56 (0.36), residues: 223 sheet: -0.27 (0.39), residues: 180 loop : -0.95 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 179 TYR 0.021 0.001 TYR A 55 PHE 0.013 0.001 PHE A 491 TRP 0.009 0.001 TRP A 435 HIS 0.004 0.001 HIS A 712 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6485) covalent geometry : angle 0.57469 ( 8926) hydrogen bonds : bond 0.03926 ( 284) hydrogen bonds : angle 4.87767 ( 781) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.257 Fit side-chains REVERT: A 73 GLU cc_start: 0.6017 (OUTLIER) cc_final: 0.5764 (tm-30) REVERT: A 133 LYS cc_start: 0.6181 (tppt) cc_final: 0.5809 (tppt) REVERT: A 472 GLU cc_start: 0.7685 (pt0) cc_final: 0.7445 (tt0) REVERT: A 473 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7506 (mp10) REVERT: A 517 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9009 (tp) REVERT: A 637 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6991 (tp30) REVERT: A 641 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7511 (t0) outliers start: 21 outliers final: 11 residues processed: 90 average time/residue: 0.7791 time to fit residues: 72.7601 Evaluate side-chains 86 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 818 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 69 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 61 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 GLN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.186516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.134458 restraints weight = 5882.036| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.38 r_work: 0.3270 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6485 Z= 0.158 Angle : 0.627 9.941 8926 Z= 0.323 Chirality : 0.046 0.297 1012 Planarity : 0.006 0.097 1041 Dihedral : 18.016 178.022 1251 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.42 % Allowed : 22.64 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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 aren not related in a simple way. whole: -0.03 (0.32), residues: 700 helix: 1.55 (0.36), residues: 221 sheet: -0.40 (0.39), residues: 183 loop : -0.92 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 167 TYR 0.021 0.001 TYR A 55 PHE 0.015 0.002 PHE A 491 TRP 0.008 0.001 TRP A 199 HIS 0.004 0.001 HIS A 849 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 6485) covalent geometry : angle 0.62708 ( 8926) hydrogen bonds : bond 0.04474 ( 284) hydrogen bonds : angle 5.05579 ( 781) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.231 Fit side-chains REVERT: A 73 GLU cc_start: 0.6063 (OUTLIER) cc_final: 0.5827 (tm-30) REVERT: A 133 LYS cc_start: 0.6242 (tppt) cc_final: 0.5839 (tppt) REVERT: A 472 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7501 (pt0) REVERT: A 473 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7614 (mp10) REVERT: A 517 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9003 (tp) REVERT: A 641 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7544 (t0) outliers start: 21 outliers final: 13 residues processed: 86 average time/residue: 0.8152 time to fit residues: 72.7886 Evaluate side-chains 88 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 678 GLN Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 818 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 0.0570 chunk 33 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.188895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.137146 restraints weight = 5828.251| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.36 r_work: 0.3301 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6485 Z= 0.122 Angle : 0.600 9.471 8926 Z= 0.309 Chirality : 0.044 0.254 1012 Planarity : 0.006 0.095 1041 Dihedral : 17.997 178.897 1251 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.09 % Allowed : 23.45 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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 aren not related in a simple way. whole: -0.01 (0.32), residues: 700 helix: 1.46 (0.36), residues: 223 sheet: -0.29 (0.39), residues: 180 loop : -0.91 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 167 TYR 0.020 0.001 TYR A 55 PHE 0.013 0.001 PHE A 491 TRP 0.009 0.001 TRP A 435 HIS 0.004 0.001 HIS A 712 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6485) covalent geometry : angle 0.60044 ( 8926) hydrogen bonds : bond 0.04109 ( 284) hydrogen bonds : angle 4.96109 ( 781) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.188 Fit side-chains REVERT: A 73 GLU cc_start: 0.6074 (OUTLIER) cc_final: 0.5808 (tm-30) REVERT: A 133 LYS cc_start: 0.6238 (tppt) cc_final: 0.5831 (tppt) REVERT: A 472 GLU cc_start: 0.7675 (pt0) cc_final: 0.7458 (pt0) REVERT: A 473 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7517 (mp10) REVERT: A 517 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9007 (tp) REVERT: A 641 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7533 (t0) outliers start: 19 outliers final: 12 residues processed: 87 average time/residue: 0.8050 time to fit residues: 72.6538 Evaluate side-chains 88 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 678 GLN Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 818 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 GLN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.184962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.137299 restraints weight = 6150.264| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.36 r_work: 0.3320 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6485 Z= 0.193 Angle : 0.675 9.502 8926 Z= 0.348 Chirality : 0.048 0.251 1012 Planarity : 0.007 0.098 1041 Dihedral : 18.055 177.033 1251 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.58 % Allowed : 22.96 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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 aren not related in a simple way. whole: -0.08 (0.32), residues: 700 helix: 1.41 (0.35), residues: 221 sheet: -0.35 (0.39), residues: 176 loop : -0.92 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 167 TYR 0.023 0.002 TYR A 55 PHE 0.017 0.002 PHE A 491 TRP 0.010 0.002 TRP A 199 HIS 0.004 0.001 HIS A 849 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 6485) covalent geometry : angle 0.67488 ( 8926) hydrogen bonds : bond 0.04865 ( 284) hydrogen bonds : angle 5.18372 ( 781) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2731.53 seconds wall clock time: 47 minutes 17.35 seconds (2837.35 seconds total)