Starting phenix.real_space_refine on Fri May 9 14:59:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kny_62466/05_2025/9kny_62466.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kny_62466/05_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_62466/05_2025/9kny_62466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kny_62466/05_2025/9kny_62466.map" model { file = "/net/cci-nas-00/data/ceres_data/9kny_62466/05_2025/9kny_62466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kny_62466/05_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-5687/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: 2.93, per 1000 atoms: 1.07 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: 0.87 Conformation dependent library (CDL) restraints added in 340.6 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: 0.29 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: 0.67 Time building geometry restraints manager: 0.96 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.370 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.060 ------------------------------------------------------------------------------- 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 : 0.299 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: 0.1984 time to fit residues: 20.6496 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 : 0.296 ------------------------------------------------------------------------------- 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: 0.9980 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4211 r_free = 0.4211 target = 0.190942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.154180 restraints weight = 4002.235| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 3.06 r_work: 0.3714 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2815 Z= 0.131 Angle : 0.546 7.671 3789 Z= 0.283 Chirality : 0.040 0.131 392 Planarity : 0.005 0.055 464 Dihedral : 16.791 114.111 494 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 5.19 % Allowed : 23.33 % 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: 0.56 (0.46), residues: 327 helix: 1.40 (0.38), residues: 178 sheet: -1.09 (0.78), residues: 43 loop : -0.66 (0.60), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 PHE 0.014 0.001 PHE A 69 TYR 0.010 0.001 TYR B 32 ARG 0.005 0.001 ARG B 113 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 166) hydrogen bonds : angle 4.44089 ( 465) SS BOND : bond 0.00664 ( 1) SS BOND : angle 1.03108 ( 2) covalent geometry : bond 0.00296 ( 2814) covalent geometry : angle 0.54586 ( 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 89 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7608 (tt0) REVERT: C 29 VAL cc_start: 0.7511 (OUTLIER) cc_final: 0.6812 (p) REVERT: C 43 LYS cc_start: 0.6540 (ttpt) cc_final: 0.6302 (ttpt) REVERT: C 102 TRP cc_start: 0.6160 (t-100) cc_final: 0.5811 (m-90) outliers start: 14 outliers final: 13 residues processed: 82 average time/residue: 0.2040 time to fit residues: 19.0458 Evaluate side-chains 84 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 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 54 GLN 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: 0.9990 chunk 31 optimal weight: 0.2980 chunk 29 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.0070 chunk 30 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 3 optimal weight: 0.0770 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 54 GLN C 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.194810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.159504 restraints weight = 3824.056| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.94 r_work: 0.3781 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 2815 Z= 0.102 Angle : 0.493 6.148 3789 Z= 0.254 Chirality : 0.039 0.125 392 Planarity : 0.005 0.061 464 Dihedral : 14.667 79.666 484 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 4.44 % Allowed : 24.07 % 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: 1.31 (0.48), residues: 327 helix: 2.05 (0.39), residues: 180 sheet: -1.32 (0.71), residues: 50 loop : -0.02 (0.67), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 36 HIS 0.003 0.001 HIS A 84 PHE 0.007 0.001 PHE A 69 TYR 0.009 0.001 TYR C 95 ARG 0.008 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03261 ( 166) hydrogen bonds : angle 4.26678 ( 465) SS BOND : bond 0.01118 ( 1) SS BOND : angle 0.13340 ( 2) covalent geometry : bond 0.00220 ( 2814) covalent geometry : angle 0.49349 ( 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 80 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7594 (tt0) REVERT: A 19 ARG cc_start: 0.7774 (ptt-90) cc_final: 0.6885 (ptt-90) REVERT: A 66 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8692 (t80) REVERT: C 4 LEU cc_start: 0.7647 (mp) cc_final: 0.7443 (tp) REVERT: C 51 ILE cc_start: 0.8424 (tt) cc_final: 0.8210 (mt) REVERT: C 96 CYS cc_start: 0.5116 (OUTLIER) cc_final: 0.3871 (m) REVERT: C 102 TRP cc_start: 0.6129 (t-100) cc_final: 0.5757 (m-90) outliers start: 12 outliers final: 8 residues processed: 75 average time/residue: 0.1958 time to fit residues: 16.8627 Evaluate side-chains 75 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL 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 96 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 31 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.191114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.155968 restraints weight = 3857.892| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.88 r_work: 0.3756 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2292 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= 0.137 Angle : 0.522 7.341 3789 Z= 0.267 Chirality : 0.041 0.125 392 Planarity : 0.005 0.060 464 Dihedral : 13.996 67.783 480 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 6.30 % Allowed : 25.19 % Favored : 68.52 % 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: 1.48 (0.48), residues: 327 helix: 2.11 (0.39), residues: 180 sheet: -1.17 (0.74), residues: 50 loop : 0.18 (0.67), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 PHE 0.016 0.001 PHE A 69 TYR 0.011 0.001 TYR C 95 ARG 0.003 0.001 ARG C 32 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 166) hydrogen bonds : angle 4.20334 ( 465) SS BOND : bond 0.00403 ( 1) SS BOND : angle 0.23418 ( 2) covalent geometry : bond 0.00318 ( 2814) covalent geometry : angle 0.52177 ( 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 80 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7610 (tt0) REVERT: A 19 ARG cc_start: 0.7827 (ptt-90) cc_final: 0.6939 (ptt-90) REVERT: C 4 LEU cc_start: 0.7694 (mp) cc_final: 0.7416 (tp) REVERT: C 43 LYS cc_start: 0.6459 (ttpt) cc_final: 0.6247 (ttpt) REVERT: C 96 CYS cc_start: 0.5352 (OUTLIER) cc_final: 0.4083 (m) outliers start: 17 outliers final: 14 residues processed: 73 average time/residue: 0.1983 time to fit residues: 16.5291 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 : 0.265 ------------------------------------------------------------------------------- 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 79 LEU 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 70 ILE Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.193121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.157738 restraints weight = 3866.230| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.93 r_work: 0.3764 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2815 Z= 0.125 Angle : 0.507 8.037 3789 Z= 0.261 Chirality : 0.040 0.126 392 Planarity : 0.005 0.059 464 Dihedral : 13.587 65.120 480 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 6.67 % Allowed : 26.30 % 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: 1.66 (0.49), residues: 327 helix: 2.18 (0.39), residues: 180 sheet: -1.13 (0.75), residues: 50 loop : 0.43 (0.68), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 PHE 0.015 0.001 PHE A 69 TYR 0.012 0.001 TYR C 95 ARG 0.008 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03327 ( 166) hydrogen bonds : angle 4.16266 ( 465) SS BOND : bond 0.00407 ( 1) SS BOND : angle 0.41680 ( 2) covalent geometry : bond 0.00285 ( 2814) covalent geometry : angle 0.50723 ( 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 81 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7606 (tt0) REVERT: C 4 LEU cc_start: 0.7662 (mp) cc_final: 0.7454 (tp) REVERT: C 43 LYS cc_start: 0.6424 (ttpt) cc_final: 0.6215 (ttpt) REVERT: C 96 CYS cc_start: 0.5356 (OUTLIER) cc_final: 0.4203 (m) outliers start: 18 outliers final: 13 residues processed: 73 average time/residue: 0.2022 time to fit residues: 16.9038 Evaluate side-chains 75 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 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 70 ILE 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: 0.8980 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 28 optimal weight: 0.0370 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.195781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.161381 restraints weight = 3844.439| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.85 r_work: 0.3791 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2815 Z= 0.101 Angle : 0.495 8.311 3789 Z= 0.253 Chirality : 0.039 0.123 392 Planarity : 0.004 0.058 464 Dihedral : 12.833 62.524 480 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 5.93 % Allowed : 25.93 % Favored : 68.15 % 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: 1.86 (0.49), residues: 327 helix: 2.29 (0.39), residues: 180 sheet: -0.98 (0.82), residues: 43 loop : 0.46 (0.66), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 0.008 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 166) hydrogen bonds : angle 4.02283 ( 465) SS BOND : bond 0.00072 ( 1) SS BOND : angle 0.46413 ( 2) covalent geometry : bond 0.00222 ( 2814) covalent geometry : angle 0.49463 ( 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 79 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: B 15 ARG cc_start: 0.7241 (ttp80) cc_final: 0.6995 (ptt90) REVERT: B 119 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7666 (tt0) REVERT: A 19 ARG cc_start: 0.7807 (ptt-90) cc_final: 0.6977 (ptt-90) REVERT: C 43 LYS cc_start: 0.6483 (ttpt) cc_final: 0.6265 (ttpt) REVERT: C 51 ILE cc_start: 0.8444 (tt) cc_final: 0.8107 (mt) REVERT: C 81 LEU cc_start: 0.7710 (mt) cc_final: 0.7273 (mt) REVERT: C 82 GLN cc_start: 0.8011 (tm130) cc_final: 0.7631 (tm-30) REVERT: C 96 CYS cc_start: 0.5210 (OUTLIER) cc_final: 0.4381 (m) outliers start: 16 outliers final: 13 residues processed: 70 average time/residue: 0.2050 time to fit residues: 16.3665 Evaluate side-chains 74 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 66 PHE Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain C residue 5 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 23 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4243 r_free = 0.4243 target = 0.194444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.160034 restraints weight = 3916.082| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.87 r_work: 0.3792 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2815 Z= 0.130 Angle : 0.530 6.503 3789 Z= 0.269 Chirality : 0.040 0.125 392 Planarity : 0.005 0.057 464 Dihedral : 12.777 61.685 480 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 5.56 % Allowed : 26.30 % Favored : 68.15 % 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: 2.16 (0.38), residues: 180 sheet: -1.27 (0.74), residues: 50 loop : 0.73 (0.72), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 36 HIS 0.005 0.001 HIS A 84 PHE 0.014 0.001 PHE A 69 TYR 0.010 0.001 TYR C 95 ARG 0.007 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03265 ( 166) hydrogen bonds : angle 4.08157 ( 465) SS BOND : bond 0.00461 ( 1) SS BOND : angle 0.70797 ( 2) covalent geometry : bond 0.00302 ( 2814) covalent geometry : angle 0.52983 ( 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 78 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7663 (tt0) REVERT: A 19 ARG cc_start: 0.7844 (ptt-90) cc_final: 0.6992 (ptt-90) REVERT: C 43 LYS cc_start: 0.6512 (ttpt) cc_final: 0.6306 (ttpt) REVERT: C 81 LEU cc_start: 0.7718 (mt) cc_final: 0.7236 (mt) outliers start: 15 outliers final: 13 residues processed: 71 average time/residue: 0.2041 time to fit residues: 16.6444 Evaluate side-chains 73 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 66 PHE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 70 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** ** 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 = 0.4235 r_free = 0.4235 target = 0.193201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.158650 restraints weight = 3810.887| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.84 r_work: 0.3778 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2815 Z= 0.132 Angle : 0.541 5.579 3789 Z= 0.275 Chirality : 0.041 0.123 392 Planarity : 0.005 0.055 464 Dihedral : 12.414 60.581 479 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: 1.69 (0.49), residues: 327 helix: 2.28 (0.38), residues: 176 sheet: -1.30 (0.73), residues: 50 loop : 0.49 (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 0.013 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 0.03375 ( 166) hydrogen bonds : angle 4.11851 ( 465) SS BOND : bond 0.00408 ( 1) SS BOND : angle 0.60066 ( 2) covalent geometry : bond 0.00306 ( 2814) covalent geometry : angle 0.54048 ( 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 76 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7629 (tt0) REVERT: C 43 LYS cc_start: 0.6538 (ttpt) cc_final: 0.6319 (ttpt) REVERT: C 51 ILE cc_start: 0.8352 (tt) cc_final: 0.7921 (mt) outliers start: 15 outliers final: 12 residues processed: 69 average time/residue: 0.1759 time to fit residues: 14.1185 Evaluate side-chains 72 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 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 22 CYS Chi-restraints excluded: chain C residue 98 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 14 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** 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 = 0.4242 r_free = 0.4242 target = 0.194073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.159673 restraints weight = 3800.608| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.86 r_work: 0.3786 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3032 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= 0.118 Angle : 0.539 8.708 3789 Z= 0.273 Chirality : 0.041 0.170 392 Planarity : 0.005 0.055 464 Dihedral : 12.136 59.730 479 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 4.07 % Allowed : 28.52 % 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: 1.61 (0.49), residues: 327 helix: 2.22 (0.38), residues: 176 sheet: -1.42 (0.71), residues: 50 loop : 0.49 (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 0.009 0.001 TYR C 95 ARG 0.007 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 166) hydrogen bonds : angle 4.08306 ( 465) SS BOND : bond 0.00237 ( 1) SS BOND : angle 0.70343 ( 2) covalent geometry : bond 0.00270 ( 2814) covalent geometry : angle 0.53857 ( 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 69 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7633 (tt0) REVERT: C 43 LYS cc_start: 0.6551 (ttpt) cc_final: 0.6335 (ttpt) REVERT: C 51 ILE cc_start: 0.8365 (tt) cc_final: 0.7948 (mt) outliers start: 11 outliers final: 11 residues processed: 62 average time/residue: 0.1987 time to fit residues: 14.2543 Evaluate side-chains 68 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 B residue 93 ASN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 54 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** ** 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 = 0.4240 r_free = 0.4240 target = 0.194172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.159615 restraints weight = 3864.269| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.89 r_work: 0.3804 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3126 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= 0.126 Angle : 0.551 7.891 3789 Z= 0.277 Chirality : 0.042 0.218 392 Planarity : 0.005 0.056 464 Dihedral : 12.079 59.524 479 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.33 % Allowed : 29.63 % 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: 1.55 (0.48), residues: 327 helix: 2.22 (0.38), residues: 176 sheet: -1.48 (0.70), residues: 50 loop : 0.38 (0.69), 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 0.012 0.001 PHE A 69 TYR 0.009 0.001 TYR A 62 ARG 0.007 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03395 ( 166) hydrogen bonds : angle 4.04211 ( 465) SS BOND : bond 0.00315 ( 1) SS BOND : angle 0.46539 ( 2) covalent geometry : bond 0.00292 ( 2814) covalent geometry : angle 0.55062 ( 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 64 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7631 (tt0) REVERT: C 43 LYS cc_start: 0.6585 (ttpt) cc_final: 0.6366 (ttpt) REVERT: C 51 ILE cc_start: 0.8412 (tt) cc_final: 0.7999 (mt) outliers start: 9 outliers final: 9 residues processed: 59 average time/residue: 0.2022 time to fit residues: 13.6342 Evaluate side-chains 64 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 B residue 93 ASN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain C residue 22 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 28 optimal weight: 0.0000 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 0.0040 chunk 2 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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** ** 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 = 0.4310 r_free = 0.4310 target = 0.198748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.164899 restraints weight = 3815.707| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.87 r_work: 0.3893 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 2815 Z= 0.106 Angle : 0.526 7.675 3789 Z= 0.267 Chirality : 0.041 0.180 392 Planarity : 0.004 0.055 464 Dihedral : 11.722 59.819 479 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.07 % Allowed : 28.52 % 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: 1.64 (0.49), residues: 327 helix: 2.31 (0.38), residues: 176 sheet: -1.49 (0.70), residues: 50 loop : 0.43 (0.70), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 PHE 0.009 0.001 PHE A 69 TYR 0.008 0.001 TYR C 95 ARG 0.006 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03295 ( 166) hydrogen bonds : angle 3.94950 ( 465) SS BOND : bond 0.00181 ( 1) SS BOND : angle 0.65487 ( 2) covalent geometry : bond 0.00238 ( 2814) covalent geometry : angle 0.52633 ( 3787) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2077.12 seconds wall clock time: 36 minutes 49.17 seconds (2209.17 seconds total)