Starting phenix.real_space_refine on Thu Dec 7 15:48:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8acb_15345/12_2023/8acb_15345.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8acb_15345/12_2023/8acb_15345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8acb_15345/12_2023/8acb_15345.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8acb_15345/12_2023/8acb_15345.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8acb_15345/12_2023/8acb_15345.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8acb_15345/12_2023/8acb_15345.pdb" } resolution = 2.6 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= 0.019 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 5 5.49 5 S 11 5.16 5 C 1116 2.51 5 N 314 2.21 5 O 369 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-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 1815 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1715 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Time building chain proxies: 1.83, per 1000 atoms: 1.01 Number of scatterers: 1815 At special positions: 0 Unit cell: (79.875, 75.615, 123.54, 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 11 16.00 P 5 15.00 O 369 8.00 N 314 7.00 C 1116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 269.6 milliseconds 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 412 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 1 sheets defined 47.3% alpha, 4.5% beta 0 base pairs and 2 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 113 through 120 removed outlier: 3.856A pdb=" N THR A 119 " --> pdb=" O GLN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 128 removed outlier: 3.581A pdb=" N VAL A 127 " --> pdb=" O GLN A 124 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 128 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 149 Processing helix chain 'A' and resid 151 through 169 removed outlier: 3.629A pdb=" N ILE A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 198 removed outlier: 4.197A pdb=" N HIS A 198 " --> pdb=" O PRO A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 209 removed outlier: 3.571A pdb=" N ILE A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 removed outlier: 3.550A pdb=" N GLU A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 235 Processing helix chain 'A' and resid 240 through 244 removed outlier: 4.417A pdb=" N ARG A 244 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 272 removed outlier: 3.581A pdb=" N ALA A 263 " --> pdb=" O ARG A 259 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 183 removed outlier: 3.607A pdb=" N GLU A 186 " --> pdb=" O ASP A 183 " (cutoff:3.500A) 61 hydrogen bonds defined for protein. 177 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 2 stacking parallelities Total time for adding SS restraints: 0.39 Time building geometry restraints manager: 0.87 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: 594 1.34 - 1.46: 308 1.46 - 1.57: 928 1.57 - 1.69: 9 1.69 - 1.81: 21 Bond restraints: 1860 Sorted by residual: bond pdb=" O5' U B 2 " pdb=" C5' U B 2 " ideal model delta sigma weight residual 1.420 1.450 -0.030 1.50e-02 4.44e+03 4.06e+00 bond pdb=" O5' U B 5 " pdb=" C5' U B 5 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.77e+00 bond pdb=" P U B 4 " pdb=" O5' U B 4 " ideal model delta sigma weight residual 1.593 1.621 -0.028 1.50e-02 4.44e+03 3.57e+00 bond pdb=" O5' U B 1 " pdb=" C5' U B 1 " ideal model delta sigma weight residual 1.420 1.447 -0.027 1.50e-02 4.44e+03 3.25e+00 bond pdb=" O5' U B 3 " pdb=" C5' U B 3 " ideal model delta sigma weight residual 1.420 1.447 -0.027 1.50e-02 4.44e+03 3.14e+00 ... (remaining 1855 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.83: 56 105.83 - 112.86: 976 112.86 - 119.89: 627 119.89 - 126.92: 858 126.92 - 133.94: 27 Bond angle restraints: 2544 Sorted by residual: angle pdb=" C3' U B 1 " pdb=" O3' U B 1 " pdb=" P U B 2 " ideal model delta sigma weight residual 120.20 109.93 10.27 1.50e+00 4.44e-01 4.68e+01 angle pdb=" O4' U B 4 " pdb=" C4' U B 4 " pdb=" C3' U B 4 " ideal model delta sigma weight residual 106.10 101.15 4.95 1.00e+00 1.00e+00 2.45e+01 angle pdb=" C4' U B 4 " pdb=" C3' U B 4 " pdb=" C2' U B 4 " ideal model delta sigma weight residual 102.60 98.80 3.80 1.00e+00 1.00e+00 1.45e+01 angle pdb=" C3' U B 2 " pdb=" O3' U B 2 " pdb=" P U B 3 " ideal model delta sigma weight residual 120.20 114.83 5.37 1.50e+00 4.44e-01 1.28e+01 angle pdb=" O3' U B 4 " pdb=" P U B 5 " pdb=" O5' U B 5 " ideal model delta sigma weight residual 104.00 108.21 -4.21 1.50e+00 4.44e-01 7.89e+00 ... (remaining 2539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.02: 1083 33.02 - 66.03: 20 66.03 - 99.05: 1 99.05 - 132.06: 0 132.06 - 165.08: 1 Dihedral angle restraints: 1105 sinusoidal: 465 harmonic: 640 Sorted by residual: dihedral pdb=" O4' U B 5 " pdb=" C1' U B 5 " pdb=" N1 U B 5 " pdb=" C2 U B 5 " ideal model delta sinusoidal sigma weight residual 200.00 34.92 165.08 1 1.50e+01 4.44e-03 8.39e+01 dihedral pdb=" C5' U B 4 " pdb=" C4' U B 4 " pdb=" C3' U B 4 " pdb=" O3' U B 4 " ideal model delta sinusoidal sigma weight residual 147.00 179.12 -32.12 1 8.00e+00 1.56e-02 2.30e+01 dihedral pdb=" C3' U B 4 " pdb=" C4' U B 4 " pdb=" O4' U B 4 " pdb=" C1' U B 4 " ideal model delta sinusoidal sigma weight residual -2.00 -34.08 32.08 1 8.00e+00 1.56e-02 2.29e+01 ... (remaining 1102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 273 0.112 - 0.223: 6 0.223 - 0.335: 1 0.335 - 0.446: 1 0.446 - 0.558: 4 Chirality restraints: 285 Sorted by residual: chirality pdb=" P U B 1 " pdb=" OP1 U B 1 " pdb=" OP2 U B 1 " pdb=" O5' U B 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.78e+00 chirality pdb=" P U B 4 " pdb=" OP1 U B 4 " pdb=" OP2 U B 4 " pdb=" O5' U B 4 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.60e+00 chirality pdb=" P U B 2 " pdb=" OP1 U B 2 " pdb=" OP2 U B 2 " pdb=" O5' U B 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.44e+00 ... (remaining 282 not shown) Planarity restraints: 321 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 103 " 0.017 5.00e-02 4.00e+02 2.55e-02 1.04e+00 pdb=" N PRO A 104 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 282 " -0.005 2.00e-02 2.50e+03 1.00e-02 1.00e+00 pdb=" C LEU A 282 " 0.017 2.00e-02 2.50e+03 pdb=" O LEU A 282 " -0.007 2.00e-02 2.50e+03 pdb=" N ASP A 283 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 121 " 0.015 5.00e-02 4.00e+02 2.24e-02 8.02e-01 pdb=" N PRO A 122 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 122 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 122 " 0.012 5.00e-02 4.00e+02 ... (remaining 318 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 420 2.79 - 3.31: 1676 3.31 - 3.84: 2816 3.84 - 4.37: 3266 4.37 - 4.90: 5307 Nonbonded interactions: 13485 Sorted by model distance: nonbonded pdb=" OD1 ASP A 239 " pdb=" OG SER A 241 " model vdw 2.257 2.440 nonbonded pdb=" O GLY A 156 " pdb=" ND2 ASN A 160 " model vdw 2.286 2.520 nonbonded pdb=" O PRO A 257 " pdb=" NZ LYS A 261 " model vdw 2.291 2.520 nonbonded pdb=" OE2 GLU A 168 " pdb=" OH TYR A 227 " model vdw 2.319 2.440 nonbonded pdb=" NE2 GLN A 205 " pdb=" OP1 U B 2 " model vdw 2.485 2.520 ... (remaining 13480 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.930 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.090 Find NCS groups from input model: 0.050 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:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 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 : 0.004 0.035 1860 Z= 0.243 Angle : 0.711 10.266 2544 Z= 0.384 Chirality : 0.079 0.558 285 Planarity : 0.003 0.025 321 Dihedral : 13.941 165.075 693 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 (0.58), residues: 218 helix: 0.34 (0.55), residues: 89 sheet: 1.47 (1.02), residues: 10 loop : -1.44 (0.61), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 179 HIS 0.001 0.000 HIS A 209 PHE 0.008 0.001 PHE A 249 TYR 0.009 0.001 TYR A 245 ARG 0.002 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.225 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 1.3981 time to fit residues: 80.8529 Evaluate side-chains 52 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.211 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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: 0.7977 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1860 Z= 0.197 Angle : 0.549 5.172 2544 Z= 0.276 Chirality : 0.040 0.148 285 Planarity : 0.004 0.036 321 Dihedral : 12.641 173.190 298 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.14 % Allowed : 12.50 % Favored : 86.36 % 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: -0.91 (0.57), residues: 218 helix: 0.35 (0.53), residues: 97 sheet: 1.37 (1.09), residues: 10 loop : -1.72 (0.61), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 179 HIS 0.001 0.000 HIS A 209 PHE 0.011 0.002 PHE A 249 TYR 0.008 0.001 TYR A 245 ARG 0.002 0.000 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.203 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 52 average time/residue: 1.5253 time to fit residues: 80.3765 Evaluate side-chains 49 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.206 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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: 0.8055 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1860 Z= 0.206 Angle : 0.547 5.617 2544 Z= 0.273 Chirality : 0.039 0.140 285 Planarity : 0.004 0.038 321 Dihedral : 12.864 178.102 298 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 2.27 % Allowed : 14.20 % Favored : 83.52 % 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: -0.79 (0.58), residues: 218 helix: 0.55 (0.54), residues: 96 sheet: 1.49 (1.29), residues: 10 loop : -1.74 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 179 HIS 0.001 0.000 HIS A 209 PHE 0.012 0.002 PHE A 249 TYR 0.009 0.001 TYR A 190 ARG 0.002 0.000 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.206 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 52 average time/residue: 1.5186 time to fit residues: 80.0426 Evaluate side-chains 51 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.214 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.8111 time to fit residues: 2.1226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 2 optimal weight: 0.0040 chunk 9 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 21 optimal weight: 0.0050 chunk 10 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 overall best weight: 1.1808 ------------------------------------------------------------------------------- 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: 0.7995 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 1860 Z= 0.136 Angle : 0.479 5.099 2544 Z= 0.237 Chirality : 0.037 0.119 285 Planarity : 0.003 0.032 321 Dihedral : 12.898 178.875 298 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.27 % Allowed : 15.34 % Favored : 82.39 % 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: -0.66 (0.58), residues: 218 helix: 0.64 (0.53), residues: 96 sheet: 1.77 (1.39), residues: 10 loop : -1.67 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 179 HIS 0.001 0.000 HIS A 209 PHE 0.009 0.001 PHE A 249 TYR 0.011 0.001 TYR A 190 ARG 0.001 0.000 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.203 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 53 average time/residue: 1.4691 time to fit residues: 78.9746 Evaluate side-chains 52 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.212 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.5686 time to fit residues: 1.8656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 15 optimal weight: 10.0000 chunk 8 optimal weight: 0.2980 chunk 18 optimal weight: 9.9990 chunk 14 optimal weight: 0.2980 chunk 0 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.7992 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 1860 Z= 0.133 Angle : 0.472 5.476 2544 Z= 0.232 Chirality : 0.036 0.110 285 Planarity : 0.003 0.030 321 Dihedral : 12.609 177.523 298 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.70 % Allowed : 16.48 % Favored : 81.82 % 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: -0.52 (0.59), residues: 218 helix: 0.74 (0.54), residues: 96 sheet: 1.96 (1.47), residues: 10 loop : -1.60 (0.62), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 179 HIS 0.001 0.000 HIS A 264 PHE 0.009 0.001 PHE A 249 TYR 0.011 0.001 TYR A 190 ARG 0.001 0.000 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.188 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 51 average time/residue: 1.5365 time to fit residues: 79.4226 Evaluate side-chains 52 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.201 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 1.5656 time to fit residues: 1.8590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 5 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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: 0.8064 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1860 Z= 0.202 Angle : 0.540 6.256 2544 Z= 0.267 Chirality : 0.039 0.136 285 Planarity : 0.004 0.034 321 Dihedral : 11.960 168.787 298 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 3.98 % Allowed : 14.77 % Favored : 81.25 % 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: -0.56 (0.59), residues: 218 helix: 0.79 (0.54), residues: 96 sheet: 1.96 (1.46), residues: 10 loop : -1.71 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 179 HIS 0.002 0.001 HIS A 209 PHE 0.011 0.002 PHE A 249 TYR 0.010 0.001 TYR A 190 ARG 0.002 0.000 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.214 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 52 average time/residue: 1.5387 time to fit residues: 81.2473 Evaluate side-chains 50 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.181 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.2411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 12 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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: 0.8064 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1860 Z= 0.190 Angle : 0.541 6.160 2544 Z= 0.267 Chirality : 0.039 0.131 285 Planarity : 0.004 0.034 321 Dihedral : 12.023 169.349 298 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 1.70 % Allowed : 17.05 % Favored : 81.25 % 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: -0.54 (0.59), residues: 218 helix: 0.81 (0.54), residues: 96 sheet: 2.02 (1.45), residues: 10 loop : -1.70 (0.62), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 179 HIS 0.002 0.001 HIS A 209 PHE 0.010 0.001 PHE A 249 TYR 0.011 0.001 TYR A 190 ARG 0.002 0.000 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.226 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 52 average time/residue: 1.6053 time to fit residues: 84.5991 Evaluate side-chains 51 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.204 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.2770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 1 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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: 0.8057 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1860 Z= 0.171 Angle : 0.519 6.166 2544 Z= 0.256 Chirality : 0.038 0.124 285 Planarity : 0.004 0.033 321 Dihedral : 11.953 168.057 298 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 2.27 % Allowed : 16.48 % Favored : 81.25 % 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: -0.44 (0.59), residues: 218 helix: 0.87 (0.54), residues: 96 sheet: 2.10 (1.46), residues: 10 loop : -1.64 (0.62), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 179 HIS 0.001 0.001 HIS A 209 PHE 0.010 0.001 PHE A 249 TYR 0.013 0.001 TYR A 190 ARG 0.001 0.000 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.210 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 52 average time/residue: 1.5631 time to fit residues: 82.3678 Evaluate side-chains 52 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.213 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.2784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 0.2980 chunk 21 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1860 Z= 0.195 Angle : 0.545 6.214 2544 Z= 0.270 Chirality : 0.039 0.136 285 Planarity : 0.004 0.034 321 Dihedral : 12.053 169.484 298 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 2.27 % Allowed : 16.48 % Favored : 81.25 % 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: -0.47 (0.59), residues: 218 helix: 0.86 (0.55), residues: 96 sheet: 2.10 (1.48), residues: 10 loop : -1.67 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 179 HIS 0.002 0.001 HIS A 209 PHE 0.010 0.001 PHE A 249 TYR 0.014 0.001 TYR A 190 ARG 0.004 0.000 ARG A 244 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.209 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 1.5265 time to fit residues: 78.9154 Evaluate side-chains 50 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.208 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.2795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 16 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1860 Z= 0.278 Angle : 0.628 7.723 2544 Z= 0.312 Chirality : 0.043 0.162 285 Planarity : 0.005 0.037 321 Dihedral : 12.262 170.322 298 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 1.70 % Allowed : 16.48 % Favored : 81.82 % 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: -0.66 (0.59), residues: 218 helix: 0.61 (0.54), residues: 98 sheet: 2.06 (1.45), residues: 10 loop : -1.72 (0.61), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 179 HIS 0.002 0.001 HIS A 209 PHE 0.012 0.002 PHE A 249 TYR 0.015 0.001 TYR A 190 ARG 0.004 0.001 ARG A 244 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.175 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 52 average time/residue: 1.4955 time to fit residues: 78.8151 Evaluate side-chains 47 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.198 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.2595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 14 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.140363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.119579 restraints weight = 2388.787| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.76 r_work: 0.3270 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 1860 Z= 0.150 Angle : 0.508 6.069 2544 Z= 0.249 Chirality : 0.038 0.119 285 Planarity : 0.003 0.032 321 Dihedral : 11.971 166.700 298 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.70 % Allowed : 17.61 % Favored : 80.68 % 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: -0.42 (0.59), residues: 218 helix: 0.89 (0.54), residues: 96 sheet: 2.15 (1.46), residues: 10 loop : -1.63 (0.62), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 179 HIS 0.001 0.001 HIS A 198 PHE 0.009 0.001 PHE A 249 TYR 0.013 0.001 TYR A 190 ARG 0.002 0.000 ARG A 244 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1637.87 seconds wall clock time: 35 minutes 3.54 seconds (2103.54 seconds total)