Starting phenix.real_space_refine on Thu Jul 24 12:44:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6q_62132/07_2025/9k6q_62132.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6q_62132/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9k6q_62132/07_2025/9k6q_62132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6q_62132/07_2025/9k6q_62132.map" model { file = "/net/cci-nas-00/data/ceres_data/9k6q_62132/07_2025/9k6q_62132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6q_62132/07_2025/9k6q_62132.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.18, per 1000 atoms: 0.83 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: 1.79 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 3.81 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: 3.23 Time building geometry restraints manager: 2.11 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: 1.040 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 24.550 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:27.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.720 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.002 TRP A 199 HIS 0.006 0.001 HIS A 168 PHE 0.013 0.002 PHE A 491 TYR 0.024 0.002 TYR A 55 ARG 0.004 0.001 ARG A 658 Details of bonding type rmsd hydrogen bonds : bond 0.16733 ( 284) hydrogen bonds : angle 7.63781 ( 781) covalent geometry : bond 0.00428 ( 6485) covalent geometry : angle 0.82552 ( 8926) *********************** 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 : 1.257 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: 2.3440 time to fit residues: 198.3594 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 : 1.379 ------------------------------------------------------------------------------- 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 60 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 0.3980 chunk 18 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.187305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.136426 restraints weight = 5889.054| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.34 r_work: 0.3300 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1154 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 : 0.622 7.273 8926 Z= 0.331 Chirality : 0.046 0.302 1012 Planarity : 0.007 0.096 1041 Dihedral : 18.283 176.727 1253 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.71 % Favored : 96.14 % Rotamer: Outliers : 1.95 % Allowed : 23.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.32), residues: 700 helix: 1.16 (0.35), residues: 222 sheet: -0.42 (0.38), residues: 184 loop : -0.81 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 435 HIS 0.007 0.001 HIS A 168 PHE 0.012 0.001 PHE A 491 TYR 0.017 0.001 TYR A 55 ARG 0.003 0.000 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.04658 ( 284) hydrogen bonds : angle 5.48420 ( 781) covalent geometry : bond 0.00305 ( 6485) covalent geometry : angle 0.62166 ( 8926) *********************** 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 86 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.687 Fit side-chains REVERT: A 98 LYS cc_start: 0.6416 (mtmm) cc_final: 0.6185 (mptt) REVERT: A 473 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7678 (mp10) REVERT: A 637 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6968 (tp30) outliers start: 12 outliers final: 5 residues processed: 82 average time/residue: 1.5692 time to fit residues: 134.0781 Evaluate side-chains 76 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 4 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.181159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.134144 restraints weight = 5933.062| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.36 r_work: 0.3239 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 6485 Z= 0.238 Angle : 0.712 9.259 8926 Z= 0.373 Chirality : 0.050 0.253 1012 Planarity : 0.007 0.105 1041 Dihedral : 18.397 175.774 1251 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.86 % Favored : 96.00 % Rotamer: Outliers : 4.40 % Allowed : 20.36 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.31), residues: 700 helix: 1.08 (0.35), residues: 228 sheet: -0.28 (0.39), residues: 176 loop : -0.89 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 199 HIS 0.005 0.001 HIS A 849 PHE 0.017 0.002 PHE A 491 TYR 0.022 0.002 TYR A 55 ARG 0.006 0.001 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.05490 ( 284) hydrogen bonds : angle 5.54465 ( 781) covalent geometry : bond 0.00540 ( 6485) covalent geometry : angle 0.71197 ( 8926) *********************** 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 100 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.622 Fit side-chains REVERT: A 98 LYS cc_start: 0.6499 (mtmm) cc_final: 0.6252 (mtpp) REVERT: A 473 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7762 (mp10) REVERT: A 637 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7055 (tp30) REVERT: A 693 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.6978 (mtpt) outliers start: 27 outliers final: 12 residues processed: 87 average time/residue: 1.5053 time to fit residues: 136.5066 Evaluate side-chains 83 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 356 LEU 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 569 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 678 GLN Chi-restraints excluded: chain A residue 693 LYS Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 756 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 10 optimal weight: 0.0870 chunk 71 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 GLN 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 = 0.4018 r_free = 0.4018 target = 0.185857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.134097 restraints weight = 5986.498| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.37 r_work: 0.3271 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1698 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= 0.130 Angle : 0.605 7.370 8926 Z= 0.318 Chirality : 0.045 0.221 1012 Planarity : 0.006 0.097 1041 Dihedral : 18.283 178.387 1251 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.71 % Favored : 96.14 % Rotamer: Outliers : 3.58 % Allowed : 20.68 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.32), residues: 700 helix: 1.41 (0.36), residues: 223 sheet: -0.24 (0.39), residues: 177 loop : -0.96 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 435 HIS 0.004 0.001 HIS A 600 PHE 0.014 0.001 PHE A 491 TYR 0.021 0.001 TYR A 55 ARG 0.003 0.000 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.04313 ( 284) hydrogen bonds : angle 5.20156 ( 781) covalent geometry : bond 0.00280 ( 6485) covalent geometry : angle 0.60533 ( 8926) *********************** 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: 22 poor density : 69 time to evaluate : 0.623 Fit side-chains REVERT: A 73 GLU cc_start: 0.5743 (OUTLIER) cc_final: 0.5377 (tm-30) REVERT: A 133 LYS cc_start: 0.6232 (tppt) cc_final: 0.5826 (tppt) REVERT: A 401 VAL cc_start: 0.7198 (OUTLIER) cc_final: 0.6954 (p) REVERT: A 473 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7755 (mp10) REVERT: A 517 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8986 (tp) REVERT: A 637 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6995 (tp30) REVERT: A 641 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7496 (t0) outliers start: 22 outliers final: 9 residues processed: 84 average time/residue: 1.4827 time to fit residues: 129.8364 Evaluate side-chains 79 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 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 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 756 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 0.0670 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.187349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.135933 restraints weight = 5869.914| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.36 r_work: 0.3296 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1789 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= 0.121 Angle : 0.584 7.554 8926 Z= 0.305 Chirality : 0.044 0.204 1012 Planarity : 0.006 0.096 1041 Dihedral : 18.082 179.170 1251 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.91 % Allowed : 20.03 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.32), residues: 700 helix: 1.54 (0.36), residues: 224 sheet: -0.25 (0.39), residues: 181 loop : -0.95 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 435 HIS 0.004 0.001 HIS A 712 PHE 0.014 0.001 PHE A 491 TYR 0.020 0.001 TYR A 55 ARG 0.003 0.000 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 284) hydrogen bonds : angle 5.01331 ( 781) covalent geometry : bond 0.00260 ( 6485) covalent geometry : angle 0.58420 ( 8926) *********************** 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: 24 poor density : 72 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: A 133 LYS cc_start: 0.6228 (tppt) cc_final: 0.5817 (tppt) REVERT: A 472 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7442 (pt0) REVERT: A 473 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7688 (mp10) REVERT: A 483 MET cc_start: 0.8736 (ttp) cc_final: 0.8418 (ttp) REVERT: A 517 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9011 (tp) REVERT: A 637 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7021 (tp30) outliers start: 24 outliers final: 8 residues processed: 88 average time/residue: 1.6708 time to fit residues: 153.1401 Evaluate side-chains 79 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR 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 591 VAL Chi-restraints excluded: chain A residue 756 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 45 optimal weight: 0.0070 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 overall best weight: 0.9804 ------------------------------------------------------------------------------- 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 = 0.4020 r_free = 0.4020 target = 0.185936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.138220 restraints weight = 5866.462| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.38 r_work: 0.3288 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6485 Z= 0.136 Angle : 0.594 7.215 8926 Z= 0.311 Chirality : 0.045 0.211 1012 Planarity : 0.006 0.096 1041 Dihedral : 18.050 178.381 1251 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.58 % Allowed : 20.85 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.32), residues: 700 helix: 1.56 (0.36), residues: 222 sheet: -0.29 (0.39), residues: 182 loop : -0.93 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 435 HIS 0.004 0.001 HIS A 712 PHE 0.014 0.001 PHE A 491 TYR 0.020 0.001 TYR A 55 ARG 0.002 0.000 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.04235 ( 284) hydrogen bonds : angle 5.00785 ( 781) covalent geometry : bond 0.00297 ( 6485) covalent geometry : angle 0.59422 ( 8926) *********************** 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: 22 poor density : 68 time to evaluate : 0.643 Fit side-chains REVERT: A 98 LYS cc_start: 0.6640 (mtmm) cc_final: 0.6274 (mptt) REVERT: A 133 LYS cc_start: 0.6292 (tppt) cc_final: 0.5905 (tppt) REVERT: A 472 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7450 (pt0) REVERT: A 473 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7694 (mp10) REVERT: A 517 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9020 (tp) REVERT: A 637 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7008 (tp30) REVERT: A 641 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7526 (t0) outliers start: 22 outliers final: 12 residues processed: 84 average time/residue: 1.7107 time to fit residues: 149.0553 Evaluate side-chains 83 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR 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 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 719 ASP Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 818 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 4 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 14 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.185761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.134002 restraints weight = 5864.937| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.36 r_work: 0.3282 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6485 Z= 0.138 Angle : 0.591 7.391 8926 Z= 0.309 Chirality : 0.044 0.210 1012 Planarity : 0.006 0.096 1041 Dihedral : 18.049 178.366 1251 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.58 % Allowed : 21.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.32), residues: 700 helix: 1.53 (0.36), residues: 222 sheet: -0.29 (0.39), residues: 182 loop : -0.90 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 435 HIS 0.004 0.001 HIS A 712 PHE 0.015 0.001 PHE A 491 TYR 0.020 0.001 TYR A 55 ARG 0.004 0.000 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.04239 ( 284) hydrogen bonds : angle 4.98829 ( 781) covalent geometry : bond 0.00305 ( 6485) covalent geometry : angle 0.59071 ( 8926) *********************** 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 94 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.561 Fit side-chains REVERT: A 98 LYS cc_start: 0.6551 (mtmm) cc_final: 0.6156 (mptt) REVERT: A 133 LYS cc_start: 0.6269 (tppt) cc_final: 0.5871 (tppt) REVERT: A 356 LEU cc_start: 0.0374 (OUTLIER) cc_final: 0.0116 (tt) REVERT: A 472 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7539 (pt0) REVERT: A 473 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7701 (mp10) REVERT: A 517 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9023 (tp) REVERT: A 637 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7023 (tp30) REVERT: A 641 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7524 (t0) outliers start: 22 outliers final: 11 residues processed: 89 average time/residue: 1.5382 time to fit residues: 142.3279 Evaluate side-chains 86 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 356 LEU 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 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 28 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.184746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.132818 restraints weight = 5853.425| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.36 r_work: 0.3273 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6485 Z= 0.159 Angle : 0.616 7.137 8926 Z= 0.322 Chirality : 0.045 0.221 1012 Planarity : 0.006 0.097 1041 Dihedral : 18.052 177.716 1251 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.42 % Allowed : 21.99 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.32), residues: 700 helix: 1.48 (0.36), residues: 222 sheet: -0.28 (0.39), residues: 177 loop : -0.94 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 199 HIS 0.004 0.001 HIS A 849 PHE 0.016 0.002 PHE A 491 TYR 0.021 0.001 TYR A 55 ARG 0.004 0.000 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.04502 ( 284) hydrogen bonds : angle 5.06497 ( 781) covalent geometry : bond 0.00357 ( 6485) covalent geometry : angle 0.61586 ( 8926) *********************** 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 93 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.670 Fit side-chains REVERT: A 98 LYS cc_start: 0.6626 (mtmm) cc_final: 0.6359 (mptt) REVERT: A 133 LYS cc_start: 0.6266 (tppt) cc_final: 0.5865 (tppt) REVERT: A 172 MET cc_start: 0.4861 (OUTLIER) cc_final: 0.4454 (ttm) REVERT: A 396 GLU cc_start: 0.7443 (tt0) cc_final: 0.7203 (tt0) REVERT: A 472 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7484 (pt0) REVERT: A 473 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7667 (mp10) REVERT: A 517 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9011 (tp) REVERT: A 641 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7532 (t70) outliers start: 21 outliers final: 12 residues processed: 88 average time/residue: 1.8722 time to fit residues: 171.4333 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 : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 356 LEU 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 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 11 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.187555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.136515 restraints weight = 6168.186| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.38 r_work: 0.3342 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6485 Z= 0.124 Angle : 0.584 7.462 8926 Z= 0.306 Chirality : 0.044 0.199 1012 Planarity : 0.006 0.095 1041 Dihedral : 18.025 179.005 1251 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.77 % Allowed : 22.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.32), residues: 700 helix: 1.51 (0.36), residues: 223 sheet: -0.24 (0.39), residues: 180 loop : -0.88 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 435 HIS 0.004 0.001 HIS A 712 PHE 0.014 0.001 PHE A 94 TYR 0.020 0.001 TYR A 55 ARG 0.002 0.000 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 284) hydrogen bonds : angle 4.93003 ( 781) covalent geometry : bond 0.00273 ( 6485) covalent geometry : angle 0.58413 ( 8926) *********************** 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 88 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.825 Fit side-chains REVERT: A 98 LYS cc_start: 0.6852 (mtmm) cc_final: 0.6416 (mptt) REVERT: A 133 LYS cc_start: 0.6286 (tppt) cc_final: 0.5928 (tppt) REVERT: A 356 LEU cc_start: -0.0254 (OUTLIER) cc_final: -0.0544 (tt) REVERT: A 473 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7588 (mp10) REVERT: A 517 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9011 (tp) REVERT: A 641 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7475 (t0) outliers start: 17 outliers final: 12 residues processed: 85 average time/residue: 1.6248 time to fit residues: 144.5859 Evaluate side-chains 85 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 356 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 62 optimal weight: 0.5980 chunk 71 optimal weight: 0.0370 chunk 59 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 0.0070 chunk 57 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 overall best weight: 0.5076 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.191814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.145715 restraints weight = 6188.070| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.31 r_work: 0.3413 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6485 Z= 0.110 Angle : 0.568 7.515 8926 Z= 0.295 Chirality : 0.043 0.176 1012 Planarity : 0.006 0.094 1041 Dihedral : 17.988 179.759 1251 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.61 % Allowed : 22.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.32), residues: 700 helix: 1.59 (0.36), residues: 223 sheet: -0.22 (0.39), residues: 180 loop : -0.84 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 211 HIS 0.004 0.001 HIS A 600 PHE 0.013 0.001 PHE A 491 TYR 0.018 0.001 TYR A 55 ARG 0.003 0.000 ARG A 460 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 284) hydrogen bonds : angle 4.75600 ( 781) covalent geometry : bond 0.00240 ( 6485) covalent geometry : angle 0.56760 ( 8926) ********************** 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: 16 poor density : 76 time to evaluate : 0.706 Fit side-chains REVERT: A 98 LYS cc_start: 0.6679 (mtmm) cc_final: 0.6110 (mmtm) REVERT: A 133 LYS cc_start: 0.6271 (tppt) cc_final: 0.5900 (tppt) REVERT: A 356 LEU cc_start: -0.0293 (OUTLIER) cc_final: -0.0634 (tt) REVERT: A 476 LYS cc_start: 0.7825 (ptpp) cc_final: 0.7467 (ttpp) REVERT: A 517 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8972 (tp) REVERT: A 641 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7363 (t0) REVERT: A 850 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7564 (mm-40) outliers start: 16 outliers final: 9 residues processed: 89 average time/residue: 1.6295 time to fit residues: 150.6988 Evaluate side-chains 86 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 356 LEU 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 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 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 3 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 757 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 = 0.4059 r_free = 0.4059 target = 0.189971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.143413 restraints weight = 6219.180| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.41 r_work: 0.3377 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6485 Z= 0.131 Angle : 0.604 9.126 8926 Z= 0.311 Chirality : 0.044 0.239 1012 Planarity : 0.006 0.095 1041 Dihedral : 17.966 179.315 1251 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.28 % Allowed : 23.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.32), residues: 700 helix: 1.48 (0.36), residues: 223 sheet: -0.23 (0.39), residues: 180 loop : -0.83 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 435 HIS 0.004 0.001 HIS A 712 PHE 0.014 0.001 PHE A 491 TYR 0.019 0.001 TYR A 55 ARG 0.005 0.000 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 284) hydrogen bonds : angle 4.88698 ( 781) covalent geometry : bond 0.00292 ( 6485) covalent geometry : angle 0.60440 ( 8926) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6356.48 seconds wall clock time: 115 minutes 17.43 seconds (6917.43 seconds total)