Starting phenix.real_space_refine on Thu Jul 18 17:27:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjp_17718/07_2024/8pjp_17718.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjp_17718/07_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjp_17718/07_2024/8pjp_17718.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjp_17718/07_2024/8pjp_17718.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjp_17718/07_2024/8pjp_17718.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjp_17718/07_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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 2.86, per 1000 atoms: 1.33 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 - 3.50 Amino acid : False - 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: 1.16 Conformation dependent library (CDL) restraints added in 401.4 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: 0.29 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: 0.52 Time building geometry restraints manager: 0.82 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: 99.59 - 106.47: 46 106.47 - 113.35: 1220 113.35 - 120.23: 700 120.23 - 127.11: 990 127.11 - 133.99: 21 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 2.440 nonbonded pdb=" NH2 ARG C 69 " pdb=" OD2 ASP C 92 " model vdw 2.456 2.520 nonbonded pdb=" N ASP C 116 " pdb=" OD1 ASP C 116 " model vdw 2.482 2.520 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 2.520 ... (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 ========== 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: 2.180 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.240 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.930 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.257 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: 0.8820 time to fit residues: 69.6132 Evaluate side-chains 64 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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: 6.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 17 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.8973 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2192 Z= 0.337 Angle : 0.609 7.409 2977 Z= 0.308 Chirality : 0.044 0.141 345 Planarity : 0.003 0.019 380 Dihedral : 4.670 28.641 340 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 7.14 % Allowed : 23.21 % 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: 0.72 (0.52), residues: 282 helix: 1.04 (0.72), residues: 59 sheet: 0.72 (0.61), residues: 72 loop : 0.25 (0.55), 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 0.001 PHE C 29 TYR 0.010 0.001 TYR C 97 ARG 0.004 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 fitting. rotamer outliers: 16 poor density : 65 time to evaluate : 0.232 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 77 average time/residue: 0.8315 time to fit residues: 65.6474 Evaluate side-chains 68 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 30 THR 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: 0.6980 chunk 25 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.8933 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2192 Z= 0.182 Angle : 0.546 7.960 2977 Z= 0.271 Chirality : 0.041 0.131 345 Planarity : 0.003 0.021 380 Dihedral : 4.261 29.969 339 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.57 % Allowed : 27.23 % Favored : 69.20 % 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: 1.20 (0.72), residues: 59 sheet: 0.87 (0.60), residues: 72 loop : 0.21 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.001 0.001 HIS C 64 PHE 0.003 0.001 PHE C 70 TYR 0.006 0.001 TYR C 117 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 68 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.218 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 66 average time/residue: 0.9253 time to fit residues: 62.5660 Evaluate side-chains 63 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 0.0170 chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 overall best weight: 2.6024 ------------------------------------------------------------------------------- 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: 0.8976 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2192 Z= 0.289 Angle : 0.597 8.632 2977 Z= 0.295 Chirality : 0.044 0.137 345 Planarity : 0.003 0.021 380 Dihedral : 4.849 38.459 339 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.57 % Allowed : 28.12 % 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: 0.67 (0.52), residues: 282 helix: 1.06 (0.72), residues: 59 sheet: 0.91 (0.61), residues: 72 loop : 0.05 (0.54), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.002 0.001 HIS A 149 PHE 0.013 0.001 PHE C 29 TYR 0.007 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 67 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.224 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 66 average time/residue: 0.9303 time to fit residues: 62.8328 Evaluate side-chains 65 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 0.0470 chunk 6 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- 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: 0.8953 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2192 Z= 0.217 Angle : 0.569 8.781 2977 Z= 0.281 Chirality : 0.042 0.132 345 Planarity : 0.003 0.021 380 Dihedral : 4.704 40.329 339 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.57 % Allowed : 29.91 % Favored : 66.52 % 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: 0.69 (0.52), residues: 282 helix: 1.09 (0.72), residues: 59 sheet: 1.13 (0.59), residues: 77 loop : -0.12 (0.54), residues: 146 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 0.012 0.001 PHE C 29 TYR 0.006 0.001 TYR C 97 ARG 0.004 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 66 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 65 average time/residue: 0.8836 time to fit residues: 58.7667 Evaluate side-chains 62 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE 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 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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: 0.8939 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2192 Z= 0.193 Angle : 0.573 9.237 2977 Z= 0.282 Chirality : 0.042 0.130 345 Planarity : 0.003 0.021 380 Dihedral : 4.665 42.419 339 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.02 % Allowed : 28.57 % Favored : 67.41 % 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: 0.75 (0.52), residues: 282 helix: 1.11 (0.73), residues: 59 sheet: 1.19 (0.59), residues: 77 loop : -0.09 (0.55), residues: 146 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 0.005 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 69 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 66 average time/residue: 0.9835 time to fit residues: 66.4932 Evaluate side-chains 64 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE 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 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 chunk 24 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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: 0.8952 moved from start: 0.3246 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= 0.226 Angle : 0.592 9.660 2977 Z= 0.291 Chirality : 0.043 0.132 345 Planarity : 0.003 0.020 380 Dihedral : 4.860 47.161 339 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.12 % Allowed : 29.46 % Favored : 67.41 % 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 (0.52), residues: 282 helix: 1.02 (0.72), residues: 59 sheet: 1.06 (0.55), residues: 87 loop : -0.05 (0.57), 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 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 65 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.8324 (p0) cc_final: 0.7936 (p0) outliers start: 7 outliers final: 5 residues processed: 65 average time/residue: 0.7967 time to fit residues: 53.0376 Evaluate side-chains 62 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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: 0.8940 moved from start: 0.3279 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= 0.209 Angle : 0.594 10.066 2977 Z= 0.292 Chirality : 0.043 0.130 345 Planarity : 0.003 0.021 380 Dihedral : 4.867 50.267 339 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.23 % Allowed : 30.36 % Favored : 67.41 % 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 (0.52), residues: 282 helix: 1.06 (0.72), residues: 59 sheet: 1.04 (0.55), residues: 87 loop : -0.01 (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 0.005 0.001 TYR C 97 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 64 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.8310 (p0) cc_final: 0.7819 (p0) outliers start: 5 outliers final: 5 residues processed: 64 average time/residue: 0.9058 time to fit residues: 59.3946 Evaluate side-chains 63 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.3980 chunk 23 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.0000 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 0.0770 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.6946 ------------------------------------------------------------------------------- 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: 0.8894 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 2192 Z= 0.167 Angle : 0.575 10.372 2977 Z= 0.282 Chirality : 0.042 0.126 345 Planarity : 0.003 0.023 380 Dihedral : 4.664 50.067 339 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.23 % Allowed : 30.36 % Favored : 67.41 % 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: 1.07 (0.53), residues: 282 helix: 1.79 (0.74), residues: 53 sheet: 1.06 (0.56), residues: 87 loop : 0.14 (0.57), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.012 0.001 PHE C 29 TYR 0.006 0.001 TYR C 82 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 67 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.8187 (p0) cc_final: 0.7849 (p0) outliers start: 5 outliers final: 6 residues processed: 67 average time/residue: 0.9417 time to fit residues: 64.5839 Evaluate side-chains 65 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 87 SER Chi-restraints excluded: chain C residue 116 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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: 0.8951 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2192 Z= 0.255 Angle : 0.634 10.359 2977 Z= 0.313 Chirality : 0.044 0.133 345 Planarity : 0.003 0.019 380 Dihedral : 5.057 55.403 339 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.23 % Allowed : 30.36 % Favored : 67.41 % 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: 0.72 (0.52), residues: 282 helix: 1.01 (0.72), residues: 59 sheet: 0.97 (0.56), residues: 87 loop : 0.01 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 108 HIS 0.002 0.000 HIS A 149 PHE 0.008 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 65 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.8236 (p0) cc_final: 0.7880 (p0) outliers start: 5 outliers final: 5 residues processed: 65 average time/residue: 0.8969 time to fit residues: 59.5939 Evaluate side-chains 65 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.9980 chunk 22 optimal weight: 0.0070 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.7600 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.080487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.052841 restraints weight = 4719.537| |-----------------------------------------------------------------------------| r_work (start): 0.2597 rms_B_bonded: 2.80 r_work: 0.2484 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2373 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2192 Z= 0.179 Angle : 0.597 10.175 2977 Z= 0.291 Chirality : 0.042 0.127 345 Planarity : 0.003 0.027 380 Dihedral : 4.812 53.955 339 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.68 % Allowed : 29.91 % Favored : 67.41 % 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: 1.05 (0.53), residues: 282 helix: 1.73 (0.74), residues: 53 sheet: 1.01 (0.57), residues: 87 loop : 0.19 (0.57), residues: 142 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 0.004 0.001 TYR A 50 ARG 0.008 0.000 ARG C 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1625.78 seconds wall clock time: 32 minutes 16.10 seconds (1936.10 seconds total)