Starting phenix.real_space_refine on Wed Jun 4 12:09:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kny_62466/06_2025/9kny_62466.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kny_62466/06_2025/9kny_62466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kny_62466/06_2025/9kny_62466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kny_62466/06_2025/9kny_62466.map" model { file = "/net/cci-nas-00/data/ceres_data/9kny_62466/06_2025/9kny_62466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kny_62466/06_2025/9kny_62466.cif" } resolution = 3.4 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= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 17 5.16 5 C 1783 2.51 5 N 460 2.21 5 O 484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 2747 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1000 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 118} Chain: "A" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 745 Classifications: {'peptide': 93} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 88} Chain: "C" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 879 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 89 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'PC8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.72, per 1000 atoms: 0.99 Number of scatterers: 2747 At special positions: 0 Unit cell: (81.51, 93.48, 86.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 3 15.00 O 484 8.00 N 460 7.00 C 1783 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 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: 0.76 Conformation dependent library (CDL) restraints added in 279.1 milliseconds 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 614 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 60.4% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'B' and resid 40 through 57 removed outlier: 3.789A pdb=" N TRP B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 68 through 86 Processing helix chain 'B' and resid 93 through 126 removed outlier: 3.688A pdb=" N HIS B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 23 removed outlier: 3.988A pdb=" N MET A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 29 removed outlier: 4.055A pdb=" N TRP A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 34 through 44 removed outlier: 3.521A pdb=" N ILE A 38 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 46 No H-bonds generated for 'chain 'A' and resid 45 through 46' Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.647A pdb=" N ILE A 50 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 73 Processing helix chain 'A' and resid 77 through 108 removed outlier: 3.695A pdb=" N PHE A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.514A pdb=" N THR C 91 " --> pdb=" O PRO C 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.104A pdb=" N GLY C 10 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N SER C 114 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL C 12 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 166 hydrogen bonds defined for protein. 465 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.65 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 409 1.30 - 1.43: 780 1.43 - 1.56: 1578 1.56 - 1.68: 18 1.68 - 1.81: 29 Bond restraints: 2814 Sorted by residual: bond pdb=" CB7 CDL B 201 " pdb=" OB8 CDL B 201 " ideal model delta sigma weight residual 1.334 1.436 -0.102 1.10e-02 8.26e+03 8.58e+01 bond pdb=" CA7 CDL B 201 " pdb=" OA8 CDL B 201 " ideal model delta sigma weight residual 1.334 1.430 -0.096 1.10e-02 8.26e+03 7.60e+01 bond pdb=" CA5 CDL B 201 " pdb=" OA6 CDL B 201 " ideal model delta sigma weight residual 1.342 1.440 -0.098 1.50e-02 4.44e+03 4.28e+01 bond pdb=" CB5 CDL B 201 " pdb=" OB6 CDL B 201 " ideal model delta sigma weight residual 1.342 1.438 -0.096 1.50e-02 4.44e+03 4.11e+01 bond pdb=" OB2 CDL B 201 " pdb=" PB2 CDL B 201 " ideal model delta sigma weight residual 1.579 1.664 -0.085 1.50e-02 4.44e+03 3.22e+01 ... (remaining 2809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 3739 3.13 - 6.25: 38 6.25 - 9.38: 7 9.38 - 12.51: 2 12.51 - 15.63: 1 Bond angle restraints: 3787 Sorted by residual: angle pdb=" C51 CDL B 201 " pdb=" CB5 CDL B 201 " pdb=" OB6 CDL B 201 " ideal model delta sigma weight residual 111.33 120.44 -9.11 1.32e+00 5.72e-01 4.75e+01 angle pdb=" C11 CDL B 201 " pdb=" CA5 CDL B 201 " pdb=" OA6 CDL B 201 " ideal model delta sigma weight residual 111.33 119.87 -8.54 1.32e+00 5.72e-01 4.17e+01 angle pdb=" C71 CDL B 201 " pdb=" CB7 CDL B 201 " pdb=" OB8 CDL B 201 " ideal model delta sigma weight residual 111.64 121.12 -9.48 1.65e+00 3.69e-01 3.32e+01 angle pdb=" CA2 CDL B 201 " pdb=" OA2 CDL B 201 " pdb=" PA1 CDL B 201 " ideal model delta sigma weight residual 121.27 115.75 5.52 1.00e+00 1.00e+00 3.05e+01 angle pdb=" C31 CDL B 201 " pdb=" CA7 CDL B 201 " pdb=" OA8 CDL B 201 " ideal model delta sigma weight residual 111.64 120.45 -8.81 1.65e+00 3.69e-01 2.86e+01 ... (remaining 3782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.66: 1558 29.66 - 59.32: 128 59.32 - 88.98: 6 88.98 - 118.64: 0 118.64 - 148.30: 1 Dihedral angle restraints: 1693 sinusoidal: 734 harmonic: 959 Sorted by residual: dihedral pdb=" C1 PC8 A 201 " pdb=" O3 PC8 A 201 " pdb=" P1 PC8 A 201 " pdb=" O4 PC8 A 201 " ideal model delta sinusoidal sigma weight residual 166.83 -44.87 -148.30 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual -86.00 -118.46 32.46 1 1.00e+01 1.00e-02 1.50e+01 dihedral pdb=" CA GLU A 49 " pdb=" CB GLU A 49 " pdb=" CG GLU A 49 " pdb=" CD GLU A 49 " ideal model delta sinusoidal sigma weight residual 60.00 118.30 -58.30 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 1690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 283 0.042 - 0.083: 83 0.083 - 0.124: 19 0.124 - 0.165: 5 0.165 - 0.207: 2 Chirality restraints: 392 Sorted by residual: chirality pdb=" C7 PC8 A 201 " pdb=" C6 PC8 A 201 " pdb=" C8 PC8 A 201 " pdb=" O7 PC8 A 201 " both_signs ideal model delta sigma weight residual False -2.32 -2.53 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA MET A 67 " pdb=" N MET A 67 " pdb=" C MET A 67 " pdb=" CB MET A 67 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.31e-01 chirality pdb=" CA VAL C 93 " pdb=" N VAL C 93 " pdb=" C VAL C 93 " pdb=" CB VAL C 93 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 389 not shown) Planarity restraints: 464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 34 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO B 35 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 35 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 35 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 29 " 0.026 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO A 30 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 24 " 0.025 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO B 25 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 25 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 25 " 0.021 5.00e-02 4.00e+02 ... (remaining 461 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 856 2.82 - 3.34: 2545 3.34 - 3.86: 4582 3.86 - 4.38: 5208 4.38 - 4.90: 8671 Nonbonded interactions: 21862 Sorted by model distance: nonbonded pdb=" NH1 ARG C 38 " pdb=" OD1 ASP C 90 " model vdw 2.299 3.120 nonbonded pdb=" NE2 GLN C 13 " pdb=" O SER C 114 " model vdw 2.326 3.120 nonbonded pdb=" NE1 TRP B 82 " pdb=" O GLY A 29 " model vdw 2.337 3.120 nonbonded pdb=" OD1 ASP C 52 " pdb=" N SER C 57 " model vdw 2.339 3.120 nonbonded pdb=" N ASP A 17 " pdb=" OD1 ASP A 17 " model vdw 2.354 3.120 ... (remaining 21857 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: 1.540 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.630 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 : 0.009 0.106 2815 Z= 0.533 Angle : 0.930 15.635 3789 Z= 0.528 Chirality : 0.044 0.207 392 Planarity : 0.005 0.045 464 Dihedral : 19.437 148.303 1076 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.44 % Allowed : 16.67 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.33 (0.42), residues: 327 helix: -0.36 (0.35), residues: 169 sheet: -1.23 (0.64), residues: 57 loop : -1.25 (0.60), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 28 HIS 0.005 0.001 HIS A 84 PHE 0.026 0.002 PHE A 69 TYR 0.018 0.002 TYR C 95 ARG 0.002 0.000 ARG A 97 Details of bonding type rmsd hydrogen bonds : bond 0.11793 ( 166) hydrogen bonds : angle 5.50693 ( 465) SS BOND : bond 0.00508 ( 1) SS BOND : angle 1.10010 ( 2) covalent geometry : bond 0.00914 ( 2814) covalent geometry : angle 0.92946 ( 3787) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 119 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7774 (tt0) REVERT: A 18 PHE cc_start: 0.6371 (t80) cc_final: 0.6046 (p90) REVERT: A 91 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7359 (mm-40) outliers start: 12 outliers final: 11 residues processed: 92 average time/residue: 0.1974 time to fit residues: 20.6458 Evaluate side-chains 85 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 98 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 0.3980 chunk 24 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN C 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.190220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.153157 restraints weight = 4005.350| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 3.07 r_work: 0.3725 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2815 Z= 0.146 Angle : 0.558 8.181 3789 Z= 0.289 Chirality : 0.041 0.133 392 Planarity : 0.005 0.054 464 Dihedral : 16.945 114.192 494 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 5.56 % Allowed : 22.96 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.48 (0.46), residues: 327 helix: 1.33 (0.38), residues: 178 sheet: -1.10 (0.78), residues: 43 loop : -0.69 (0.60), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 PHE 0.014 0.001 PHE A 69 TYR 0.011 0.002 TYR C 95 ARG 0.005 0.001 ARG B 113 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 166) hydrogen bonds : angle 4.47307 ( 465) SS BOND : bond 0.00403 ( 1) SS BOND : angle 0.87317 ( 2) covalent geometry : bond 0.00332 ( 2814) covalent geometry : angle 0.55796 ( 3787) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7596 (tt0) REVERT: C 29 VAL cc_start: 0.7482 (OUTLIER) cc_final: 0.6757 (p) REVERT: C 43 LYS cc_start: 0.6525 (ttpt) cc_final: 0.6293 (ttpt) REVERT: C 46 GLU cc_start: 0.6129 (mm-30) cc_final: 0.5861 (mm-30) REVERT: C 81 LEU cc_start: 0.7843 (tt) cc_final: 0.7616 (tp) REVERT: C 102 TRP cc_start: 0.6146 (t-100) cc_final: 0.5721 (m-90) outliers start: 15 outliers final: 13 residues processed: 86 average time/residue: 0.1980 time to fit residues: 19.5265 Evaluate side-chains 87 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 98 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 3 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 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 54 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.193097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.157538 restraints weight = 3788.649| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.86 r_work: 0.3767 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2815 Z= 0.120 Angle : 0.513 5.594 3789 Z= 0.264 Chirality : 0.040 0.126 392 Planarity : 0.005 0.063 464 Dihedral : 14.849 77.895 486 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.81 % Allowed : 24.44 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.15 (0.48), residues: 327 helix: 1.94 (0.39), residues: 180 sheet: -1.38 (0.71), residues: 50 loop : -0.16 (0.65), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 PHE 0.011 0.001 PHE A 69 TYR 0.010 0.001 TYR C 95 ARG 0.002 0.000 ARG C 38 Details of bonding type rmsd hydrogen bonds : bond 0.03425 ( 166) hydrogen bonds : angle 4.30029 ( 465) SS BOND : bond 0.01068 ( 1) SS BOND : angle 0.29574 ( 2) covalent geometry : bond 0.00271 ( 2814) covalent geometry : angle 0.51314 ( 3787) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: B 16 LEU cc_start: 0.7852 (mm) cc_final: 0.7613 (mm) REVERT: B 119 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7602 (tt0) REVERT: A 19 ARG cc_start: 0.7821 (ptt-90) cc_final: 0.6907 (ptt-90) REVERT: A 91 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7442 (mm-40) REVERT: C 4 LEU cc_start: 0.7738 (mp) cc_final: 0.7476 (tp) REVERT: C 81 LEU cc_start: 0.7696 (tt) cc_final: 0.7097 (tp) REVERT: C 96 CYS cc_start: 0.5189 (OUTLIER) cc_final: 0.3926 (m) outliers start: 13 outliers final: 11 residues processed: 76 average time/residue: 0.2112 time to fit residues: 18.3687 Evaluate side-chains 79 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 31 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 22 optimal weight: 30.0000 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 0.0770 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN ** C 82 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 = 0.4242 r_free = 0.4242 target = 0.193608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.157713 restraints weight = 3989.523| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 3.10 r_work: 0.3767 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2815 Z= 0.110 Angle : 0.494 7.372 3789 Z= 0.253 Chirality : 0.039 0.124 392 Planarity : 0.004 0.059 464 Dihedral : 14.083 67.009 480 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 6.67 % Allowed : 24.44 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.52 (0.49), residues: 327 helix: 2.14 (0.39), residues: 180 sheet: -1.17 (0.72), residues: 50 loop : 0.19 (0.68), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 PHE 0.011 0.001 PHE A 69 TYR 0.010 0.001 TYR C 95 ARG 0.004 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03268 ( 166) hydrogen bonds : angle 4.15991 ( 465) SS BOND : bond 0.00474 ( 1) SS BOND : angle 0.31228 ( 2) covalent geometry : bond 0.00248 ( 2814) covalent geometry : angle 0.49444 ( 3787) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7617 (tt0) REVERT: A 19 ARG cc_start: 0.7826 (ptt-90) cc_final: 0.6959 (ptt-90) REVERT: C 4 LEU cc_start: 0.7687 (mp) cc_final: 0.7483 (tp) REVERT: C 81 LEU cc_start: 0.7462 (tt) cc_final: 0.7131 (tp) REVERT: C 96 CYS cc_start: 0.5305 (OUTLIER) cc_final: 0.4199 (m) outliers start: 18 outliers final: 14 residues processed: 77 average time/residue: 0.2013 time to fit residues: 17.7216 Evaluate side-chains 78 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 98 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.193899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.158341 restraints weight = 3864.998| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.98 r_work: 0.3759 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2815 Z= 0.120 Angle : 0.514 7.197 3789 Z= 0.263 Chirality : 0.040 0.125 392 Planarity : 0.004 0.057 464 Dihedral : 13.602 64.483 480 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 7.78 % Allowed : 24.81 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.69 (0.48), residues: 327 helix: 2.18 (0.39), residues: 180 sheet: -0.95 (0.81), residues: 43 loop : 0.28 (0.65), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 PHE 0.013 0.001 PHE A 69 TYR 0.011 0.001 TYR C 95 ARG 0.007 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 166) hydrogen bonds : angle 4.11682 ( 465) SS BOND : bond 0.00576 ( 1) SS BOND : angle 0.14647 ( 2) covalent geometry : bond 0.00277 ( 2814) covalent geometry : angle 0.51423 ( 3787) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7635 (tt0) REVERT: C 51 ILE cc_start: 0.8442 (tt) cc_final: 0.8114 (mt) REVERT: C 81 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6938 (tp) REVERT: C 96 CYS cc_start: 0.5384 (OUTLIER) cc_final: 0.4317 (m) outliers start: 21 outliers final: 15 residues processed: 72 average time/residue: 0.2108 time to fit residues: 17.3087 Evaluate side-chains 78 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 0.0070 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.194689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.159634 restraints weight = 3886.829| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.91 r_work: 0.3805 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2815 Z= 0.113 Angle : 0.516 7.704 3789 Z= 0.260 Chirality : 0.039 0.123 392 Planarity : 0.004 0.056 464 Dihedral : 13.037 62.005 480 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 6.67 % Allowed : 25.93 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.80 (0.48), residues: 327 helix: 2.37 (0.39), residues: 176 sheet: -1.06 (0.80), residues: 43 loop : 0.29 (0.64), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 36 HIS 0.005 0.001 HIS A 84 PHE 0.009 0.001 PHE A 69 TYR 0.010 0.001 TYR C 95 ARG 0.010 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03255 ( 166) hydrogen bonds : angle 4.12347 ( 465) SS BOND : bond 0.00172 ( 1) SS BOND : angle 0.80419 ( 2) covalent geometry : bond 0.00259 ( 2814) covalent geometry : angle 0.51534 ( 3787) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: B 15 ARG cc_start: 0.7269 (ttp80) cc_final: 0.7014 (ptt90) REVERT: B 119 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7627 (tt0) REVERT: A 19 ARG cc_start: 0.7831 (ptt-90) cc_final: 0.6996 (ptt-90) REVERT: C 51 ILE cc_start: 0.8411 (tt) cc_final: 0.8120 (mt) outliers start: 18 outliers final: 14 residues processed: 73 average time/residue: 0.2170 time to fit residues: 18.0179 Evaluate side-chains 77 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 70 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 23 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 0.0870 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.193439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.157685 restraints weight = 3961.924| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.96 r_work: 0.3777 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2815 Z= 0.118 Angle : 0.510 5.764 3789 Z= 0.259 Chirality : 0.039 0.123 392 Planarity : 0.004 0.055 464 Dihedral : 12.580 61.249 479 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 5.93 % Allowed : 26.30 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.76 (0.49), residues: 327 helix: 2.38 (0.39), residues: 176 sheet: -1.37 (0.71), residues: 50 loop : 0.49 (0.70), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 36 HIS 0.005 0.001 HIS A 84 PHE 0.011 0.001 PHE A 69 TYR 0.009 0.001 TYR C 95 ARG 0.008 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03309 ( 166) hydrogen bonds : angle 4.11278 ( 465) SS BOND : bond 0.00305 ( 1) SS BOND : angle 0.71630 ( 2) covalent geometry : bond 0.00272 ( 2814) covalent geometry : angle 0.51017 ( 3787) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 15 ARG cc_start: 0.7298 (ttp80) cc_final: 0.7004 (ptt90) REVERT: B 119 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7646 (tt0) REVERT: A 19 ARG cc_start: 0.7832 (ptt-90) cc_final: 0.6982 (ptt-90) outliers start: 16 outliers final: 14 residues processed: 71 average time/residue: 0.2181 time to fit residues: 17.5777 Evaluate side-chains 78 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 98 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 0.0170 chunk 9 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.195141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.159955 restraints weight = 3810.516| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.91 r_work: 0.3809 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2815 Z= 0.114 Angle : 0.502 5.754 3789 Z= 0.257 Chirality : 0.039 0.121 392 Planarity : 0.004 0.055 464 Dihedral : 12.096 59.562 479 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 5.56 % Allowed : 27.41 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.72 (0.49), residues: 327 helix: 2.37 (0.38), residues: 176 sheet: -1.51 (0.69), residues: 50 loop : 0.50 (0.71), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 28 HIS 0.005 0.001 HIS A 84 PHE 0.008 0.001 PHE A 69 TYR 0.009 0.001 TYR C 95 ARG 0.006 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03307 ( 166) hydrogen bonds : angle 4.06776 ( 465) SS BOND : bond 0.00186 ( 1) SS BOND : angle 0.73619 ( 2) covalent geometry : bond 0.00261 ( 2814) covalent geometry : angle 0.50184 ( 3787) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 15 ARG cc_start: 0.7283 (ttp80) cc_final: 0.7005 (ptt90) REVERT: B 119 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7656 (tt0) REVERT: C 32 ARG cc_start: 0.8353 (mmm-85) cc_final: 0.8037 (mmm-85) REVERT: C 51 ILE cc_start: 0.8398 (tt) cc_final: 0.7987 (mt) outliers start: 15 outliers final: 10 residues processed: 69 average time/residue: 0.1956 time to fit residues: 15.5740 Evaluate side-chains 72 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 8 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.193868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.159142 restraints weight = 3829.647| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.89 r_work: 0.3810 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2815 Z= 0.117 Angle : 0.522 7.576 3789 Z= 0.265 Chirality : 0.039 0.123 392 Planarity : 0.004 0.055 464 Dihedral : 11.834 59.967 476 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 5.19 % Allowed : 27.41 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.66 (0.49), residues: 327 helix: 2.33 (0.38), residues: 176 sheet: -1.64 (0.68), residues: 50 loop : 0.52 (0.70), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 36 HIS 0.005 0.001 HIS A 84 PHE 0.011 0.001 PHE A 69 TYR 0.010 0.001 TYR A 62 ARG 0.008 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 166) hydrogen bonds : angle 4.05279 ( 465) SS BOND : bond 0.00163 ( 1) SS BOND : angle 1.08242 ( 2) covalent geometry : bond 0.00267 ( 2814) covalent geometry : angle 0.52153 ( 3787) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 15 ARG cc_start: 0.7309 (ttp80) cc_final: 0.7015 (ptt90) REVERT: B 119 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7623 (tt0) REVERT: C 51 ILE cc_start: 0.8398 (tt) cc_final: 0.8012 (mt) outliers start: 14 outliers final: 12 residues processed: 69 average time/residue: 0.1967 time to fit residues: 15.7524 Evaluate side-chains 73 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 98 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN ** A 33 ASN ** 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 = 0.4268 r_free = 0.4268 target = 0.194797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.158056 restraints weight = 4088.282| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 3.20 r_work: 0.3761 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2815 Z= 0.129 Angle : 0.536 7.497 3789 Z= 0.274 Chirality : 0.040 0.123 392 Planarity : 0.004 0.055 464 Dihedral : 11.859 59.033 476 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 5.19 % Allowed : 28.15 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.60 (0.49), residues: 327 helix: 2.26 (0.38), residues: 176 sheet: -1.69 (0.68), residues: 50 loop : 0.54 (0.70), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 28 HIS 0.005 0.001 HIS A 84 PHE 0.014 0.001 PHE A 69 TYR 0.010 0.001 TYR A 62 ARG 0.007 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 166) hydrogen bonds : angle 4.06940 ( 465) SS BOND : bond 0.00148 ( 1) SS BOND : angle 1.08877 ( 2) covalent geometry : bond 0.00298 ( 2814) covalent geometry : angle 0.53552 ( 3787) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 15 ARG cc_start: 0.7341 (ttp80) cc_final: 0.7032 (ptt90) REVERT: B 119 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7620 (tt0) REVERT: A 92 LEU cc_start: 0.7340 (mm) cc_final: 0.7099 (mm) REVERT: C 51 ILE cc_start: 0.8413 (tt) cc_final: 0.8048 (mt) outliers start: 14 outliers final: 13 residues processed: 68 average time/residue: 0.1810 time to fit residues: 14.2532 Evaluate side-chains 74 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 98 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 28 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.195272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.160950 restraints weight = 3825.192| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.84 r_work: 0.3782 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 2815 Z= 0.211 Angle : 1.354 59.050 3789 Z= 0.795 Chirality : 0.043 0.259 392 Planarity : 0.005 0.055 464 Dihedral : 11.887 59.034 476 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 4.44 % Allowed : 28.52 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.62 (0.49), residues: 327 helix: 2.28 (0.39), residues: 176 sheet: -1.69 (0.68), residues: 50 loop : 0.55 (0.69), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 94 HIS 0.005 0.001 HIS A 84 PHE 0.013 0.001 PHE A 69 TYR 0.011 0.001 TYR A 62 ARG 0.008 0.001 ARG C 32 Details of bonding type rmsd hydrogen bonds : bond 0.03800 ( 166) hydrogen bonds : angle 4.12180 ( 465) SS BOND : bond 0.00202 ( 1) SS BOND : angle 0.96802 ( 2) covalent geometry : bond 0.00397 ( 2814) covalent geometry : angle 1.35413 ( 3787) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2151.13 seconds wall clock time: 37 minutes 36.79 seconds (2256.79 seconds total)