Starting phenix.real_space_refine on Wed Sep 17 03:16:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kny_62466/09_2025/9kny_62466.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kny_62466/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9kny_62466/09_2025/9kny_62466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kny_62466/09_2025/9kny_62466.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kny_62466/09_2025/9kny_62466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kny_62466/09_2025/9kny_62466.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.08, per 1000 atoms: 0.39 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: 0.31 Conformation dependent library (CDL) restraints added in 101.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.10 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: 0.43 Time building geometry restraints manager: 0.35 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: 2.370 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.840 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.680 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.002 0.000 ARG A 97 TYR 0.018 0.002 TYR C 95 PHE 0.026 0.002 PHE A 69 TRP 0.013 0.002 TRP A 28 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00914 ( 2814) covalent geometry : angle 0.92946 ( 3787) SS BOND : bond 0.00508 ( 1) SS BOND : angle 1.10010 ( 2) hydrogen bonds : bond 0.11793 ( 166) hydrogen bonds : angle 5.50693 ( 465) *********************** 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 : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 119 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7775 (tt0) REVERT: A 18 PHE cc_start: 0.6371 (t80) cc_final: 0.6045 (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: 0.1002 time to fit residues: 10.4231 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 : 0.104 ------------------------------------------------------------------------------- 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 24 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.0570 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.0970 overall best weight: 0.5900 ------------------------------------------------------------------------------- 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 = 0.4221 r_free = 0.4221 target = 0.192115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.155414 restraints weight = 4080.680| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 3.16 r_work: 0.3736 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2815 Z= 0.121 Angle : 0.537 7.163 3789 Z= 0.278 Chirality : 0.040 0.131 392 Planarity : 0.005 0.053 464 Dihedral : 16.647 113.984 494 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.81 % Allowed : 22.59 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.46), residues: 327 helix: 1.43 (0.38), residues: 178 sheet: -1.18 (0.71), residues: 50 loop : -0.67 (0.63), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 113 TYR 0.010 0.001 TYR B 32 PHE 0.010 0.001 PHE A 69 TRP 0.020 0.001 TRP C 36 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 2814) covalent geometry : angle 0.53688 ( 3787) SS BOND : bond 0.00662 ( 1) SS BOND : angle 1.24195 ( 2) hydrogen bonds : bond 0.03560 ( 166) hydrogen bonds : angle 4.42243 ( 465) *********************** 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 87 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 LYS cc_start: 0.7649 (tttt) cc_final: 0.7441 (tppt) REVERT: B 119 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7581 (tt0) REVERT: C 29 VAL cc_start: 0.7495 (OUTLIER) cc_final: 0.6795 (p) REVERT: C 43 LYS cc_start: 0.6497 (ttpt) cc_final: 0.6259 (ttpt) REVERT: C 102 TRP cc_start: 0.6128 (t-100) cc_final: 0.5733 (m-90) outliers start: 13 outliers final: 11 residues processed: 79 average time/residue: 0.0970 time to fit residues: 8.7224 Evaluate side-chains 81 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.070 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 0.0020 chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- 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 = 0.4227 r_free = 0.4227 target = 0.193427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.158234 restraints weight = 3910.171| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.93 r_work: 0.3755 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2117 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= 0.118 Angle : 0.513 6.228 3789 Z= 0.265 Chirality : 0.040 0.127 392 Planarity : 0.006 0.068 464 Dihedral : 14.847 84.699 482 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.81 % Allowed : 23.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.48), residues: 327 helix: 1.92 (0.39), residues: 180 sheet: -1.42 (0.70), residues: 50 loop : -0.03 (0.67), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 72 TYR 0.011 0.001 TYR C 95 PHE 0.011 0.001 PHE A 69 TRP 0.015 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 2814) covalent geometry : angle 0.51289 ( 3787) SS BOND : bond 0.00595 ( 1) SS BOND : angle 0.33976 ( 2) hydrogen bonds : bond 0.03390 ( 166) hydrogen bonds : angle 4.32345 ( 465) *********************** 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 81 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.107 Fit side-chains revert: symmetry clash REVERT: B 19 LYS cc_start: 0.7685 (tttt) cc_final: 0.7476 (tppt) REVERT: B 119 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7591 (tt0) REVERT: A 19 ARG cc_start: 0.7801 (ptt-90) cc_final: 0.6937 (ptt-90) REVERT: A 66 PHE cc_start: 0.9223 (OUTLIER) cc_final: 0.8690 (t80) REVERT: C 51 ILE cc_start: 0.8440 (tt) cc_final: 0.8198 (mt) REVERT: C 102 TRP cc_start: 0.6199 (t-100) cc_final: 0.5878 (m-90) outliers start: 13 outliers final: 10 residues processed: 76 average time/residue: 0.0757 time to fit residues: 6.6709 Evaluate side-chains 76 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.067 ------------------------------------------------------------------------------- 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 96 CYS Chi-restraints excluded: chain C residue 98 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 14 optimal weight: 0.2980 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.194275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.158738 restraints weight = 3888.388| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.91 r_work: 0.3780 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2395 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= 0.111 Angle : 0.502 7.873 3789 Z= 0.258 Chirality : 0.040 0.141 392 Planarity : 0.005 0.060 464 Dihedral : 13.697 68.606 479 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 6.67 % Allowed : 24.07 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.49), residues: 327 helix: 2.12 (0.39), residues: 180 sheet: -1.17 (0.76), residues: 50 loop : 0.24 (0.70), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 19 TYR 0.011 0.001 TYR C 95 PHE 0.013 0.001 PHE A 69 TRP 0.015 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 2814) covalent geometry : angle 0.50207 ( 3787) SS BOND : bond 0.00217 ( 1) SS BOND : angle 0.57029 ( 2) hydrogen bonds : bond 0.03248 ( 166) hydrogen bonds : angle 4.17947 ( 465) *********************** 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 83 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7621 (tt0) REVERT: A 19 ARG cc_start: 0.7841 (ptt-90) cc_final: 0.6969 (ptt-90) REVERT: A 91 GLN cc_start: 0.7646 (mm-40) cc_final: 0.7437 (mm-40) REVERT: C 4 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7368 (tp) REVERT: C 43 LYS cc_start: 0.6369 (ttpt) cc_final: 0.6158 (ttpt) outliers start: 18 outliers final: 13 residues processed: 75 average time/residue: 0.0819 time to fit residues: 7.0668 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 : 0.071 ------------------------------------------------------------------------------- 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 4 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL 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 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4233 r_free = 0.4233 target = 0.193465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.158679 restraints weight = 3840.563| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.83 r_work: 0.3781 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2600 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= 0.117 Angle : 0.503 8.384 3789 Z= 0.259 Chirality : 0.040 0.126 392 Planarity : 0.005 0.059 464 Dihedral : 13.126 65.210 479 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 7.41 % Allowed : 23.33 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.49), residues: 327 helix: 2.18 (0.39), residues: 180 sheet: -1.18 (0.84), residues: 43 loop : 0.26 (0.67), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 19 TYR 0.012 0.001 TYR C 95 PHE 0.014 0.001 PHE A 69 TRP 0.013 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 2814) covalent geometry : angle 0.50313 ( 3787) SS BOND : bond 0.00580 ( 1) SS BOND : angle 0.83400 ( 2) hydrogen bonds : bond 0.03310 ( 166) hydrogen bonds : angle 4.13308 ( 465) *********************** 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: 20 poor density : 64 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7628 (tt0) REVERT: A 102 GLU cc_start: 0.5833 (OUTLIER) cc_final: 0.5624 (mp0) REVERT: C 4 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7481 (tp) REVERT: C 43 LYS cc_start: 0.6397 (ttpt) cc_final: 0.6193 (ttpt) REVERT: C 51 ILE cc_start: 0.8446 (tt) cc_final: 0.8112 (mt) REVERT: C 81 LEU cc_start: 0.7790 (mt) cc_final: 0.7358 (mt) outliers start: 20 outliers final: 15 residues processed: 73 average time/residue: 0.0852 time to fit residues: 7.1612 Evaluate side-chains 77 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.092 ------------------------------------------------------------------------------- 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 A residue 102 GLU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 5 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.189302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.153395 restraints weight = 3855.789| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.87 r_work: 0.3731 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2815 Z= 0.181 Angle : 0.573 9.724 3789 Z= 0.294 Chirality : 0.042 0.131 392 Planarity : 0.005 0.058 464 Dihedral : 13.288 62.895 479 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 6.30 % Allowed : 24.07 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.49), residues: 327 helix: 2.08 (0.39), residues: 180 sheet: -1.47 (0.81), residues: 43 loop : 0.26 (0.65), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 19 TYR 0.016 0.002 TYR C 95 PHE 0.022 0.002 PHE A 69 TRP 0.009 0.001 TRP A 28 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 2814) covalent geometry : angle 0.57330 ( 3787) SS BOND : bond 0.01043 ( 1) SS BOND : angle 0.74444 ( 2) hydrogen bonds : bond 0.03598 ( 166) hydrogen bonds : angle 4.29135 ( 465) *********************** 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 81 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.092 Fit side-chains revert: symmetry clash REVERT: B 16 LEU cc_start: 0.7953 (mm) cc_final: 0.7731 (mm) REVERT: B 119 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7625 (tt0) REVERT: A 102 GLU cc_start: 0.5846 (OUTLIER) cc_final: 0.5613 (mp0) REVERT: C 4 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7536 (tp) REVERT: C 81 LEU cc_start: 0.7752 (mt) cc_final: 0.7346 (mt) outliers start: 17 outliers final: 14 residues processed: 72 average time/residue: 0.0792 time to fit residues: 6.6521 Evaluate side-chains 76 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.111 ------------------------------------------------------------------------------- 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 A residue 102 GLU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 5 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4240 r_free = 0.4240 target = 0.194378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.159364 restraints weight = 3814.827| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.85 r_work: 0.3785 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2818 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= 0.114 Angle : 0.519 9.591 3789 Z= 0.266 Chirality : 0.040 0.124 392 Planarity : 0.004 0.058 464 Dihedral : 12.573 61.579 479 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 5.93 % Allowed : 25.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.49), residues: 327 helix: 2.20 (0.39), residues: 180 sheet: -1.49 (0.81), residues: 43 loop : 0.41 (0.67), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 19 TYR 0.013 0.001 TYR C 95 PHE 0.013 0.001 PHE A 69 TRP 0.011 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 2814) covalent geometry : angle 0.51882 ( 3787) SS BOND : bond 0.00220 ( 1) SS BOND : angle 0.82880 ( 2) hydrogen bonds : bond 0.03269 ( 166) hydrogen bonds : angle 4.14356 ( 465) *********************** 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: 16 poor density : 62 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 15 ARG cc_start: 0.7336 (ttp80) cc_final: 0.7021 (ptt90) REVERT: B 119 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7622 (tt0) REVERT: A 66 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8730 (t80) REVERT: A 102 GLU cc_start: 0.5713 (OUTLIER) cc_final: 0.5486 (mp0) REVERT: C 51 ILE cc_start: 0.8413 (tt) cc_final: 0.8045 (mt) REVERT: C 81 LEU cc_start: 0.7694 (mt) cc_final: 0.7280 (mt) REVERT: C 82 GLN cc_start: 0.8051 (tm130) cc_final: 0.7844 (tm-30) outliers start: 16 outliers final: 12 residues processed: 69 average time/residue: 0.0943 time to fit residues: 7.4019 Evaluate side-chains 73 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.097 ------------------------------------------------------------------------------- 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 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 A residue 102 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 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 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.193458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.159025 restraints weight = 3877.857| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.84 r_work: 0.3779 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2815 Z= 0.122 Angle : 0.529 9.268 3789 Z= 0.268 Chirality : 0.040 0.124 392 Planarity : 0.005 0.057 464 Dihedral : 12.395 60.809 479 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.49), residues: 327 helix: 2.36 (0.39), residues: 176 sheet: -1.45 (0.86), residues: 41 loop : 0.20 (0.66), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 19 TYR 0.012 0.001 TYR C 95 PHE 0.012 0.001 PHE A 69 TRP 0.008 0.001 TRP C 36 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 2814) covalent geometry : angle 0.52927 ( 3787) SS BOND : bond 0.00450 ( 1) SS BOND : angle 0.71960 ( 2) hydrogen bonds : bond 0.03288 ( 166) hydrogen bonds : angle 4.17448 ( 465) *********************** 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 78 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: B 15 ARG cc_start: 0.7340 (ttp80) cc_final: 0.7032 (ptt90) REVERT: B 119 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7628 (tt0) REVERT: C 51 ILE cc_start: 0.8432 (tt) cc_final: 0.8072 (mt) REVERT: C 81 LEU cc_start: 0.7627 (mt) cc_final: 0.7272 (mt) outliers start: 15 outliers final: 14 residues processed: 70 average time/residue: 0.0892 time to fit residues: 7.1405 Evaluate side-chains 73 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.099 ------------------------------------------------------------------------------- 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 30 THR Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 14 optimal weight: 0.0170 chunk 12 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 40.0000 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 82 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 = 0.194022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.159005 restraints weight = 3966.602| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.93 r_work: 0.3804 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2815 Z= 0.107 Angle : 0.545 8.459 3789 Z= 0.275 Chirality : 0.041 0.209 392 Planarity : 0.005 0.055 464 Dihedral : 12.047 60.011 479 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 5.19 % Allowed : 26.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.49), residues: 327 helix: 2.33 (0.38), residues: 176 sheet: -1.40 (0.86), residues: 41 loop : 0.22 (0.66), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 19 TYR 0.011 0.001 TYR C 95 PHE 0.009 0.001 PHE A 69 TRP 0.009 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 2814) covalent geometry : angle 0.54441 ( 3787) SS BOND : bond 0.00486 ( 1) SS BOND : angle 0.98408 ( 2) hydrogen bonds : bond 0.03291 ( 166) hydrogen bonds : angle 4.11799 ( 465) *********************** 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 : 0.108 Fit side-chains revert: symmetry clash REVERT: B 15 ARG cc_start: 0.7309 (ttp80) cc_final: 0.7035 (ptt90) REVERT: B 119 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7610 (tt0) REVERT: A 89 VAL cc_start: 0.7628 (t) cc_final: 0.7408 (t) REVERT: C 51 ILE cc_start: 0.8435 (tt) cc_final: 0.8082 (mt) REVERT: C 81 LEU cc_start: 0.7559 (mt) cc_final: 0.7229 (mt) outliers start: 14 outliers final: 10 residues processed: 70 average time/residue: 0.0859 time to fit residues: 6.9311 Evaluate side-chains 71 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.187 ------------------------------------------------------------------------------- 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 83 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.195534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.159453 restraints weight = 3932.741| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.97 r_work: 0.3823 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2815 Z= 0.150 Angle : 0.597 11.891 3789 Z= 0.297 Chirality : 0.043 0.208 392 Planarity : 0.005 0.055 464 Dihedral : 12.242 59.777 476 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 4.07 % Allowed : 26.30 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.49), residues: 327 helix: 2.16 (0.39), residues: 176 sheet: -1.52 (0.81), residues: 43 loop : 0.29 (0.66), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 19 TYR 0.015 0.002 TYR C 95 PHE 0.014 0.002 PHE A 69 TRP 0.008 0.001 TRP A 28 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 2814) covalent geometry : angle 0.59673 ( 3787) SS BOND : bond 0.00569 ( 1) SS BOND : angle 0.79272 ( 2) hydrogen bonds : bond 0.03620 ( 166) hydrogen bonds : angle 4.21684 ( 465) ********************** 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 72 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.067 Fit side-chains revert: symmetry clash REVERT: B 16 LEU cc_start: 0.7926 (mm) cc_final: 0.7707 (mm) REVERT: B 119 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7636 (tt0) REVERT: C 81 LEU cc_start: 0.7606 (mt) cc_final: 0.7277 (mt) outliers start: 11 outliers final: 10 residues processed: 67 average time/residue: 0.0716 time to fit residues: 5.5748 Evaluate side-chains 71 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.102 ------------------------------------------------------------------------------- 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 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 30 THR Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 18 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 3 optimal weight: 0.0060 chunk 11 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 0.0570 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 15 optimal weight: 0.0030 overall best weight: 0.3924 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.194600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.159509 restraints weight = 3792.110| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.89 r_work: 0.3832 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.142 2815 Z= 0.250 Angle : 1.438 59.199 3789 Z= 0.873 Chirality : 0.044 0.241 392 Planarity : 0.005 0.055 464 Dihedral : 12.268 59.804 476 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 4.07 % Allowed : 27.04 % Favored : 68.89 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.49), residues: 327 helix: 2.18 (0.39), residues: 176 sheet: -1.53 (0.81), residues: 43 loop : 0.32 (0.66), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 19 TYR 0.014 0.001 TYR C 95 PHE 0.013 0.001 PHE A 69 TRP 0.019 0.001 TRP B 94 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 2814) covalent geometry : angle 1.43835 ( 3787) SS BOND : bond 0.00524 ( 1) SS BOND : angle 1.47794 ( 2) hydrogen bonds : bond 0.03871 ( 166) hydrogen bonds : angle 4.22791 ( 465) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1050.87 seconds wall clock time: 18 minutes 39.83 seconds (1119.83 seconds total)