Starting phenix.real_space_refine on Fri Dec 27 04:36:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pjp_17718/12_2024/8pjp_17718.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pjp_17718/12_2024/8pjp_17718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pjp_17718/12_2024/8pjp_17718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pjp_17718/12_2024/8pjp_17718.map" model { file = "/net/cci-nas-00/data/ceres_data/8pjp_17718/12_2024/8pjp_17718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pjp_17718/12_2024/8pjp_17718.cif" } resolution = 2.92 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= 0.002 sd= 0.048 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 1 5.49 5 S 9 5.16 5 C 1342 2.51 5 N 371 2.21 5 O 434 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 2157 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1197 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 931 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'G3P': 1, 'WKE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.97, per 1000 atoms: 1.38 Number of scatterers: 2157 At special positions: 0 Unit cell: (61.06, 71.38, 111.8, 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 9 16.00 P 1 15.00 O 434 8.00 N 371 7.00 C 1342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 154 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 98 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 279.9 milliseconds 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 516 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 5 sheets defined 26.2% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 2 through 18 removed outlier: 3.523A pdb=" N LEU A 6 " --> pdb=" O THR A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 42 removed outlier: 4.376A pdb=" N TYR A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 55 removed outlier: 3.569A pdb=" N VAL A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 146 through 150 Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.517A pdb=" N THR C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 113 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 83 removed outlier: 3.797A pdb=" N SER A 79 " --> pdb=" O GLN A 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 125 removed outlier: 3.511A pdb=" N ALA A 135 " --> pdb=" O THR A 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 6 through 9 removed outlier: 4.091A pdb=" N THR C 80 " --> pdb=" O ASP C 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.986A pdb=" N ILE C 36 " --> pdb=" O CYS C 52 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N CYS C 52 " --> pdb=" O ILE C 36 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TRP C 38 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 13 through 14 removed outlier: 7.034A pdb=" N ALA C 100 " --> pdb=" O ASP C 116 " (cutoff:3.500A) 95 hydrogen bonds defined for protein. 249 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: 0.53 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 709 1.34 - 1.46: 348 1.46 - 1.57: 1121 1.57 - 1.69: 1 1.69 - 1.81: 13 Bond restraints: 2192 Sorted by residual: bond pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " ideal model delta sigma weight residual 1.726 1.609 0.117 2.00e-02 2.50e+03 3.44e+01 bond pdb=" C6 WKE A 202 " pdb=" O6 WKE A 202 " ideal model delta sigma weight residual 1.401 1.433 -0.032 2.00e-02 2.50e+03 2.48e+00 bond pdb=" C8 WKE A 202 " pdb=" C9 WKE A 202 " ideal model delta sigma weight residual 1.531 1.500 0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C10 WKE A 202 " pdb=" O5 WKE A 202 " ideal model delta sigma weight residual 1.405 1.432 -0.027 2.00e-02 2.50e+03 1.79e+00 bond pdb=" C9 WKE A 202 " pdb=" O4 WKE A 202 " ideal model delta sigma weight residual 1.404 1.431 -0.027 2.00e-02 2.50e+03 1.79e+00 ... (remaining 2187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 2941 1.82 - 3.64: 25 3.64 - 5.46: 6 5.46 - 7.28: 4 7.28 - 9.10: 1 Bond angle restraints: 2977 Sorted by residual: angle pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " pdb=" O4P G3P A 201 " ideal model delta sigma weight residual 100.65 109.75 -9.10 3.00e+00 1.11e-01 9.20e+00 angle pdb=" O2P G3P A 201 " pdb=" P G3P A 201 " pdb=" O4P G3P A 201 " ideal model delta sigma weight residual 115.71 109.69 6.02 3.00e+00 1.11e-01 4.02e+00 angle pdb=" C SER A 62 " pdb=" N SER A 63 " pdb=" CA SER A 63 " ideal model delta sigma weight residual 122.60 119.64 2.96 1.56e+00 4.11e-01 3.59e+00 angle pdb=" O3P G3P A 201 " pdb=" P G3P A 201 " pdb=" O4P G3P A 201 " ideal model delta sigma weight residual 115.20 109.66 5.54 3.00e+00 1.11e-01 3.42e+00 angle pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " pdb=" O3P G3P A 201 " ideal model delta sigma weight residual 104.20 109.74 -5.54 3.00e+00 1.11e-01 3.41e+00 ... (remaining 2972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 1147 16.87 - 33.73: 119 33.73 - 50.60: 43 50.60 - 67.46: 7 67.46 - 84.33: 3 Dihedral angle restraints: 1319 sinusoidal: 507 harmonic: 812 Sorted by residual: dihedral pdb=" CB CYS C 24 " pdb=" SG CYS C 24 " pdb=" SG CYS C 98 " pdb=" CB CYS C 98 " ideal model delta sinusoidal sigma weight residual 93.00 55.87 37.13 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CB GLU A 35 " pdb=" CG GLU A 35 " pdb=" CD GLU A 35 " pdb=" OE1 GLU A 35 " ideal model delta sinusoidal sigma weight residual 0.00 -84.33 84.33 1 3.00e+01 1.11e-03 9.61e+00 dihedral pdb=" N LYS A 101 " pdb=" CA LYS A 101 " pdb=" CB LYS A 101 " pdb=" CG LYS A 101 " ideal model delta sinusoidal sigma weight residual -60.00 -113.55 53.55 3 1.50e+01 4.44e-03 9.21e+00 ... (remaining 1316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 212 0.025 - 0.050: 69 0.050 - 0.074: 35 0.074 - 0.099: 13 0.099 - 0.124: 16 Chirality restraints: 345 Sorted by residual: chirality pdb=" CA ILE C 105 " pdb=" N ILE C 105 " pdb=" C ILE C 105 " pdb=" CB ILE C 105 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA VAL C 95 " pdb=" N VAL C 95 " pdb=" C VAL C 95 " pdb=" CB VAL C 95 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.46e-01 chirality pdb=" CA VAL A 80 " pdb=" N VAL A 80 " pdb=" C VAL A 80 " pdb=" CB VAL A 80 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.42e-01 ... (remaining 342 not shown) Planarity restraints: 380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7 WKE A 202 " 0.053 2.00e-02 2.50e+03 4.32e-02 2.34e+01 pdb=" C8 WKE A 202 " -0.015 2.00e-02 2.50e+03 pdb=" C9 WKE A 202 " 0.040 2.00e-02 2.50e+03 pdb=" N1 WKE A 202 " -0.068 2.00e-02 2.50e+03 pdb=" O3 WKE A 202 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N WKE A 202 " -0.019 2.00e-02 2.50e+03 1.21e-02 1.83e+00 pdb=" C3 WKE A 202 " 0.014 2.00e-02 2.50e+03 pdb=" C4 WKE A 202 " -0.004 2.00e-02 2.50e+03 pdb=" C5 WKE A 202 " -0.004 2.00e-02 2.50e+03 pdb=" O1 WKE A 202 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 21 " -0.015 5.00e-02 4.00e+02 2.29e-02 8.42e-01 pdb=" N PRO A 22 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " -0.013 5.00e-02 4.00e+02 ... (remaining 377 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 794 2.87 - 3.38: 1665 3.38 - 3.89: 3277 3.89 - 4.39: 3602 4.39 - 4.90: 6594 Nonbonded interactions: 15932 Sorted by model distance: nonbonded pdb=" O ASP C 32 " pdb=" OG SER C 55 " model vdw 2.365 3.040 nonbonded pdb=" NH2 ARG C 69 " pdb=" OD2 ASP C 92 " model vdw 2.456 3.120 nonbonded pdb=" N ASP C 116 " pdb=" OD1 ASP C 116 " model vdw 2.482 3.120 nonbonded pdb=" C3 G3P A 201 " pdb=" O1 G3P A 201 " model vdw 2.541 2.752 nonbonded pdb=" OE2 GLU A 49 " pdb=" ND2 ASN A 53 " model vdw 2.542 3.120 ... (remaining 15927 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: 2.350 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.880 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 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 : 0.003 0.117 2192 Z= 0.203 Angle : 0.529 9.098 2977 Z= 0.245 Chirality : 0.040 0.124 345 Planarity : 0.003 0.043 380 Dihedral : 15.916 84.330 797 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.34 % Allowed : 18.75 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.81 (0.52), residues: 282 helix: 1.00 (0.70), residues: 59 sheet: 0.81 (0.60), residues: 71 loop : 0.35 (0.55), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.002 0.000 PHE A 1 TYR 0.005 0.000 TYR C 97 ARG 0.001 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.256 Fit side-chains REVERT: A 132 THR cc_start: 0.9216 (p) cc_final: 0.9013 (t) outliers start: 3 outliers final: 1 residues processed: 77 average time/residue: 0.9349 time to fit residues: 73.7818 Evaluate side-chains 64 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 2192 Z= 0.419 Angle : 0.649 6.692 2977 Z= 0.331 Chirality : 0.045 0.145 345 Planarity : 0.003 0.020 380 Dihedral : 4.863 31.730 340 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 6.25 % Allowed : 23.21 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.52), residues: 282 helix: 0.95 (0.71), residues: 59 sheet: 0.68 (0.61), residues: 72 loop : 0.19 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.002 0.001 HIS A 149 PHE 0.012 0.001 PHE C 29 TYR 0.010 0.001 TYR C 97 ARG 0.003 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 142 ASP cc_start: 0.8392 (p0) cc_final: 0.7973 (p0) outliers start: 14 outliers final: 7 residues processed: 77 average time/residue: 0.9379 time to fit residues: 74.0840 Evaluate side-chains 69 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 2192 Z= 0.415 Angle : 0.645 7.529 2977 Z= 0.327 Chirality : 0.045 0.146 345 Planarity : 0.003 0.022 380 Dihedral : 5.077 41.668 339 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.91 % Allowed : 24.55 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.51), residues: 282 helix: 0.94 (0.70), residues: 59 sheet: 0.75 (0.61), residues: 72 loop : -0.10 (0.53), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 108 HIS 0.002 0.001 HIS A 149 PHE 0.004 0.001 PHE C 70 TYR 0.007 0.001 TYR C 97 ARG 0.002 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 142 ASP cc_start: 0.8418 (p0) cc_final: 0.7986 (p0) outliers start: 11 outliers final: 8 residues processed: 71 average time/residue: 0.9641 time to fit residues: 70.1880 Evaluate side-chains 68 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 2192 Z= 0.379 Angle : 0.647 8.349 2977 Z= 0.322 Chirality : 0.045 0.146 345 Planarity : 0.003 0.022 380 Dihedral : 5.255 49.911 339 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.02 % Allowed : 27.68 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.52), residues: 282 helix: 0.87 (0.69), residues: 59 sheet: 0.92 (0.63), residues: 72 loop : -0.14 (0.53), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 108 HIS 0.002 0.001 HIS A 149 PHE 0.012 0.002 PHE C 29 TYR 0.008 0.001 TYR C 97 ARG 0.004 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 142 ASP cc_start: 0.8470 (p0) cc_final: 0.8074 (p0) REVERT: C 75 ASP cc_start: 0.8487 (t0) cc_final: 0.8086 (t0) REVERT: C 78 LYS cc_start: 0.8611 (ptpp) cc_final: 0.8298 (ptpp) outliers start: 9 outliers final: 8 residues processed: 73 average time/residue: 0.9515 time to fit residues: 71.1909 Evaluate side-chains 67 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 5 optimal weight: 0.0670 chunk 15 optimal weight: 0.0770 chunk 6 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 overall best weight: 1.4080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2192 Z= 0.196 Angle : 0.586 9.210 2977 Z= 0.292 Chirality : 0.042 0.133 345 Planarity : 0.003 0.021 380 Dihedral : 4.745 49.354 339 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.57 % Allowed : 26.79 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.62 (0.53), residues: 282 helix: 1.09 (0.71), residues: 59 sheet: 1.11 (0.61), residues: 77 loop : -0.21 (0.56), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.012 0.001 PHE C 29 TYR 0.005 0.001 TYR C 97 ARG 0.003 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.8468 (p0) cc_final: 0.8107 (p0) REVERT: C 75 ASP cc_start: 0.8518 (t0) cc_final: 0.8121 (t0) REVERT: C 78 LYS cc_start: 0.8587 (ptpp) cc_final: 0.8340 (ptpp) outliers start: 8 outliers final: 7 residues processed: 69 average time/residue: 1.0228 time to fit residues: 72.2418 Evaluate side-chains 67 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 116 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.0010 chunk 19 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2192 Z= 0.215 Angle : 0.607 9.132 2977 Z= 0.298 Chirality : 0.042 0.133 345 Planarity : 0.003 0.022 380 Dihedral : 4.767 51.132 339 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.02 % Allowed : 27.23 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.71 (0.53), residues: 282 helix: 1.12 (0.71), residues: 59 sheet: 1.11 (0.56), residues: 87 loop : -0.19 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.011 0.001 PHE C 29 TYR 0.006 0.001 TYR C 97 ARG 0.004 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.8492 (p0) cc_final: 0.8139 (p0) REVERT: C 75 ASP cc_start: 0.8510 (t0) cc_final: 0.8101 (t0) REVERT: C 78 LYS cc_start: 0.8595 (ptpp) cc_final: 0.8342 (ptpp) outliers start: 9 outliers final: 7 residues processed: 68 average time/residue: 1.0329 time to fit residues: 71.9950 Evaluate side-chains 67 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 2192 Z= 0.366 Angle : 0.658 9.235 2977 Z= 0.328 Chirality : 0.045 0.143 345 Planarity : 0.003 0.020 380 Dihedral : 5.333 57.745 339 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.46 % Allowed : 27.68 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.50 (0.52), residues: 282 helix: 0.97 (0.70), residues: 59 sheet: 0.96 (0.56), residues: 87 loop : -0.31 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 108 HIS 0.002 0.001 HIS A 149 PHE 0.010 0.001 PHE C 29 TYR 0.008 0.001 TYR C 97 ARG 0.004 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.8466 (p0) cc_final: 0.8125 (p0) REVERT: C 75 ASP cc_start: 0.8544 (t0) cc_final: 0.8123 (t0) REVERT: C 78 LYS cc_start: 0.8588 (ptpp) cc_final: 0.8305 (ptpp) outliers start: 10 outliers final: 9 residues processed: 68 average time/residue: 1.0101 time to fit residues: 70.3393 Evaluate side-chains 68 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.0870 chunk 23 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2192 Z= 0.182 Angle : 0.610 9.885 2977 Z= 0.301 Chirality : 0.042 0.130 345 Planarity : 0.003 0.021 380 Dihedral : 4.799 54.253 339 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.68 % Allowed : 31.25 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.74 (0.53), residues: 282 helix: 1.15 (0.72), residues: 59 sheet: 1.11 (0.57), residues: 87 loop : -0.15 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.011 0.001 PHE C 29 TYR 0.004 0.001 TYR A 50 ARG 0.004 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.8450 (p0) cc_final: 0.8044 (p0) REVERT: C 75 ASP cc_start: 0.8461 (t0) cc_final: 0.8038 (t0) REVERT: C 78 LYS cc_start: 0.8559 (ptpp) cc_final: 0.8305 (ptpp) outliers start: 6 outliers final: 6 residues processed: 67 average time/residue: 1.0016 time to fit residues: 68.7823 Evaluate side-chains 65 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 116 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 6 optimal weight: 0.0040 chunk 20 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2192 Z= 0.196 Angle : 0.632 10.463 2977 Z= 0.315 Chirality : 0.042 0.130 345 Planarity : 0.003 0.023 380 Dihedral : 4.779 55.407 339 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.68 % Allowed : 31.25 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.53), residues: 282 helix: 1.11 (0.73), residues: 59 sheet: 1.11 (0.57), residues: 87 loop : -0.03 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.003 0.001 PHE C 70 TYR 0.007 0.001 TYR C 117 ARG 0.005 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.8376 (p0) cc_final: 0.8061 (p0) REVERT: C 40 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.7393 (ttm170) REVERT: C 75 ASP cc_start: 0.8478 (t0) cc_final: 0.8066 (t0) REVERT: C 78 LYS cc_start: 0.8561 (ptpp) cc_final: 0.8322 (ptpp) outliers start: 6 outliers final: 5 residues processed: 67 average time/residue: 1.0968 time to fit residues: 75.1287 Evaluate side-chains 67 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 14 optimal weight: 0.0770 chunk 19 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 2192 Z= 0.259 Angle : 0.672 10.298 2977 Z= 0.333 Chirality : 0.044 0.135 345 Planarity : 0.003 0.021 380 Dihedral : 5.006 57.911 339 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.12 % Allowed : 29.91 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.70 (0.53), residues: 282 helix: 0.95 (0.72), residues: 59 sheet: 1.04 (0.57), residues: 87 loop : -0.05 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.009 0.001 PHE C 29 TYR 0.006 0.001 TYR C 97 ARG 0.005 0.000 ARG C 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.8382 (p0) cc_final: 0.8045 (p0) REVERT: C 40 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.7417 (ttm170) REVERT: C 75 ASP cc_start: 0.8483 (t0) cc_final: 0.8068 (t0) REVERT: C 78 LYS cc_start: 0.8584 (ptpp) cc_final: 0.8345 (ptpp) outliers start: 7 outliers final: 6 residues processed: 67 average time/residue: 1.0254 time to fit residues: 70.3015 Evaluate side-chains 68 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.0570 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 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 = 0.3141 r_free = 0.3141 target = 0.079019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.051682 restraints weight = 4763.709| |-----------------------------------------------------------------------------| r_work (start): 0.2572 rms_B_bonded: 2.81 r_work: 0.2456 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2344 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 2192 Z= 0.201 Angle : 0.646 10.393 2977 Z= 0.320 Chirality : 0.042 0.129 345 Planarity : 0.003 0.023 380 Dihedral : 4.748 55.740 339 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.12 % Allowed : 29.91 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.54), residues: 282 helix: 0.98 (0.72), residues: 59 sheet: 1.06 (0.58), residues: 87 loop : -0.00 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.003 0.001 PHE C 70 TYR 0.005 0.001 TYR C 117 ARG 0.005 0.000 ARG C 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1746.00 seconds wall clock time: 32 minutes 8.63 seconds (1928.63 seconds total)