Starting phenix.real_space_refine on Wed Jun 4 16:46:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hj9_34835/06_2025/8hj9_34835_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hj9_34835/06_2025/8hj9_34835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hj9_34835/06_2025/8hj9_34835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hj9_34835/06_2025/8hj9_34835.map" model { file = "/net/cci-nas-00/data/ceres_data/8hj9_34835/06_2025/8hj9_34835_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hj9_34835/06_2025/8hj9_34835_neut.cif" } resolution = 3.12 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 2083 2.51 5 N 553 2.21 5 O 621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3274 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3226 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 20, 'TRANS': 395} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.01, per 1000 atoms: 0.92 Number of scatterers: 3274 At special positions: 0 Unit cell: (67.048, 75.922, 70.992, 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 14 16.00 P 3 15.00 O 621 8.00 N 553 7.00 C 2083 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 436.6 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 758 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 56.5% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 Processing helix chain 'A' and resid 24 through 33 Processing helix chain 'A' and resid 79 through 96 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 149 through 165 removed outlier: 3.568A pdb=" N MET A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 removed outlier: 4.041A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.908A pdb=" N ALA A 306 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 339 through 344 removed outlier: 3.536A pdb=" N ASN A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 361 removed outlier: 4.479A pdb=" N VAL A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 392 Processing helix chain 'A' and resid 394 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 6.376A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLY A 71 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ILE A 108 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 279 removed outlier: 6.405A pdb=" N ILE A 215 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA A 241 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) 191 hydrogen bonds defined for protein. 549 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: 0.96 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1063 1.34 - 1.46: 676 1.46 - 1.57: 1580 1.57 - 1.69: 5 1.69 - 1.81: 27 Bond restraints: 3351 Sorted by residual: bond pdb=" O2B NAP A 501 " pdb=" P2B NAP A 501 " ideal model delta sigma weight residual 1.736 1.615 0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" C1D NAP A 501 " pdb=" O4D NAP A 501 " ideal model delta sigma weight residual 1.375 1.427 -0.052 2.00e-02 2.50e+03 6.80e+00 bond pdb=" C5D NAP A 501 " pdb=" O5D NAP A 501 " ideal model delta sigma weight residual 1.403 1.450 -0.047 2.00e-02 2.50e+03 5.54e+00 bond pdb=" O5D NAP A 501 " pdb=" PN NAP A 501 " ideal model delta sigma weight residual 1.649 1.604 0.045 2.00e-02 2.50e+03 5.07e+00 bond pdb=" O3 NAP A 501 " pdb=" PA NAP A 501 " ideal model delta sigma weight residual 1.647 1.605 0.042 2.00e-02 2.50e+03 4.48e+00 ... (remaining 3346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 4397 1.56 - 3.12: 136 3.12 - 4.68: 23 4.68 - 6.24: 3 6.24 - 7.79: 2 Bond angle restraints: 4561 Sorted by residual: angle pdb=" C VAL A 146 " pdb=" N TYR A 147 " pdb=" CA TYR A 147 " ideal model delta sigma weight residual 123.47 127.83 -4.36 1.53e+00 4.27e-01 8.13e+00 angle pdb=" C2B NAP A 501 " pdb=" O2B NAP A 501 " pdb=" P2B NAP A 501 " ideal model delta sigma weight residual 117.19 109.40 7.79 3.00e+00 1.11e-01 6.75e+00 angle pdb=" N GLY A 219 " pdb=" CA GLY A 219 " pdb=" C GLY A 219 " ideal model delta sigma weight residual 113.18 107.69 5.49 2.37e+00 1.78e-01 5.37e+00 angle pdb=" N VAL A 97 " pdb=" CA VAL A 97 " pdb=" C VAL A 97 " ideal model delta sigma weight residual 112.83 110.54 2.29 9.90e-01 1.02e+00 5.34e+00 angle pdb=" N ASP A 145 " pdb=" CA ASP A 145 " pdb=" C ASP A 145 " ideal model delta sigma weight residual 108.19 110.98 -2.79 1.29e+00 6.01e-01 4.69e+00 ... (remaining 4556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 1780 17.07 - 34.15: 174 34.15 - 51.22: 51 51.22 - 68.29: 17 68.29 - 85.36: 10 Dihedral angle restraints: 2032 sinusoidal: 843 harmonic: 1189 Sorted by residual: dihedral pdb=" CA TYR A 101 " pdb=" C TYR A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual 180.00 162.79 17.21 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CB LYS A 32 " pdb=" CG LYS A 32 " pdb=" CD LYS A 32 " pdb=" CE LYS A 32 " ideal model delta sinusoidal sigma weight residual -180.00 -122.52 -57.48 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CG LYS A 214 " pdb=" CD LYS A 214 " pdb=" CE LYS A 214 " pdb=" NZ LYS A 214 " ideal model delta sinusoidal sigma weight residual -60.00 -115.05 55.05 3 1.50e+01 4.44e-03 9.32e+00 ... (remaining 2029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 290 0.027 - 0.054: 120 0.054 - 0.081: 43 0.081 - 0.108: 37 0.108 - 0.135: 11 Chirality restraints: 501 Sorted by residual: chirality pdb=" CA ILE A 37 " pdb=" N ILE A 37 " pdb=" C ILE A 37 " pdb=" CB ILE A 37 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE A 108 " pdb=" N ILE A 108 " pdb=" C ILE A 108 " pdb=" CB ILE A 108 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.66e-01 chirality pdb=" CA ILE A 313 " pdb=" N ILE A 313 " pdb=" C ILE A 313 " pdb=" CB ILE A 313 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 498 not shown) Planarity restraints: 579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAP A 501 " -0.032 2.00e-02 2.50e+03 7.06e-02 9.96e+01 pdb=" C2N NAP A 501 " 0.113 2.00e-02 2.50e+03 pdb=" C3N NAP A 501 " 0.032 2.00e-02 2.50e+03 pdb=" C4N NAP A 501 " 0.087 2.00e-02 2.50e+03 pdb=" C5N NAP A 501 " -0.037 2.00e-02 2.50e+03 pdb=" C6N NAP A 501 " -0.059 2.00e-02 2.50e+03 pdb=" C7N NAP A 501 " -0.113 2.00e-02 2.50e+03 pdb=" N1N NAP A 501 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO A 142 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO A 150 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " -0.020 5.00e-02 4.00e+02 ... (remaining 576 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 549 2.77 - 3.30: 3323 3.30 - 3.83: 5835 3.83 - 4.37: 6712 4.37 - 4.90: 11533 Nonbonded interactions: 27952 Sorted by model distance: nonbonded pdb=" OH TYR A 408 " pdb=" O LYS A 419 " model vdw 2.234 3.040 nonbonded pdb=" NE1 TRP A 263 " pdb=" O LYS A 271 " model vdw 2.255 3.120 nonbonded pdb=" OG1 THR A 68 " pdb=" OD1 ASP A 140 " model vdw 2.257 3.040 nonbonded pdb=" OD2 ASP A 244 " pdb=" OG SER A 269 " model vdw 2.281 3.040 nonbonded pdb=" O ASP A 209 " pdb=" NZ LYS A 213 " model vdw 2.290 3.120 ... (remaining 27947 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: 0.800 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.400 Find NCS groups from input model: 0.040 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:3.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 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 0.121 3351 Z= 0.207 Angle : 0.648 7.795 4561 Z= 0.363 Chirality : 0.042 0.135 501 Planarity : 0.005 0.071 579 Dihedral : 16.737 85.364 1274 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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: 1.80 (0.43), residues: 414 helix: 2.39 (0.35), residues: 205 sheet: 0.15 (0.69), residues: 64 loop : -0.00 (0.57), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 263 HIS 0.005 0.001 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.019 0.001 TYR A 250 ARG 0.002 0.000 ARG A 16 Details of bonding type rmsd hydrogen bonds : bond 0.12091 ( 191) hydrogen bonds : angle 4.83940 ( 549) covalent geometry : bond 0.00398 ( 3351) covalent geometry : angle 0.64814 ( 4561) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.6037 (mpp) cc_final: 0.5769 (mmt) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1418 time to fit residues: 10.2031 Evaluate side-chains 43 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.155446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.131380 restraints weight = 7167.481| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.98 r_work: 0.3708 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3351 Z= 0.133 Angle : 0.487 6.810 4561 Z= 0.251 Chirality : 0.042 0.130 501 Planarity : 0.004 0.047 579 Dihedral : 9.575 63.786 517 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.21 % Allowed : 6.36 % Favored : 92.42 % 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: 1.78 (0.43), residues: 414 helix: 2.38 (0.35), residues: 210 sheet: -0.21 (0.66), residues: 70 loop : 0.12 (0.61), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.007 0.002 HIS A 388 PHE 0.007 0.001 PHE A 381 TYR 0.015 0.002 TYR A 250 ARG 0.001 0.000 ARG A 58 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 191) hydrogen bonds : angle 4.27986 ( 549) covalent geometry : bond 0.00301 ( 3351) covalent geometry : angle 0.48689 ( 4561) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.393 Fit side-chains REVERT: A 153 MET cc_start: 0.6789 (mpp) cc_final: 0.6314 (mmt) REVERT: A 230 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7338 (mm) outliers start: 4 outliers final: 2 residues processed: 49 average time/residue: 0.1295 time to fit residues: 8.2572 Evaluate side-chains 46 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 291 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 22 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.154672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.130745 restraints weight = 7022.314| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.92 r_work: 0.3703 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3351 Z= 0.122 Angle : 0.465 5.080 4561 Z= 0.238 Chirality : 0.041 0.128 501 Planarity : 0.004 0.051 579 Dihedral : 8.100 58.990 517 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.82 % Allowed : 8.48 % Favored : 89.70 % 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: 1.76 (0.43), residues: 414 helix: 2.37 (0.35), residues: 209 sheet: -0.15 (0.67), residues: 70 loop : 0.05 (0.60), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 63 HIS 0.009 0.002 HIS A 388 PHE 0.006 0.001 PHE A 381 TYR 0.011 0.001 TYR A 132 ARG 0.003 0.000 ARG A 396 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 191) hydrogen bonds : angle 4.13026 ( 549) covalent geometry : bond 0.00276 ( 3351) covalent geometry : angle 0.46521 ( 4561) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.402 Fit side-chains REVERT: A 153 MET cc_start: 0.6936 (mpp) cc_final: 0.6404 (mmt) REVERT: A 230 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7268 (mm) REVERT: A 259 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7656 (pm20) outliers start: 6 outliers final: 2 residues processed: 49 average time/residue: 0.1288 time to fit residues: 8.2183 Evaluate side-chains 47 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 291 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 20.0000 chunk 4 optimal weight: 0.0270 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.155366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.131690 restraints weight = 7158.748| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.96 r_work: 0.3716 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3351 Z= 0.103 Angle : 0.445 7.255 4561 Z= 0.227 Chirality : 0.041 0.129 501 Planarity : 0.004 0.051 579 Dihedral : 7.670 59.019 517 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.42 % Allowed : 10.91 % Favored : 86.67 % 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: 1.82 (0.43), residues: 414 helix: 2.44 (0.35), residues: 209 sheet: -0.10 (0.67), residues: 70 loop : 0.04 (0.59), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.008 0.001 HIS A 388 PHE 0.011 0.001 PHE A 381 TYR 0.018 0.001 TYR A 250 ARG 0.001 0.000 ARG A 396 Details of bonding type rmsd hydrogen bonds : bond 0.03148 ( 191) hydrogen bonds : angle 4.06504 ( 549) covalent geometry : bond 0.00230 ( 3351) covalent geometry : angle 0.44484 ( 4561) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.6992 (mpp) cc_final: 0.6611 (mmt) REVERT: A 193 GLN cc_start: 0.9232 (tp-100) cc_final: 0.8780 (tp-100) REVERT: A 230 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7289 (mm) REVERT: A 259 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7535 (pm20) outliers start: 8 outliers final: 3 residues processed: 53 average time/residue: 0.1220 time to fit residues: 8.4514 Evaluate side-chains 50 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 291 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.152272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.127689 restraints weight = 7153.703| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.95 r_work: 0.3661 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3351 Z= 0.150 Angle : 0.484 6.252 4561 Z= 0.251 Chirality : 0.042 0.127 501 Planarity : 0.004 0.051 579 Dihedral : 7.274 55.467 517 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.82 % Allowed : 13.33 % Favored : 84.85 % 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: 1.68 (0.43), residues: 414 helix: 2.32 (0.34), residues: 208 sheet: -0.24 (0.66), residues: 71 loop : 0.03 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 30 HIS 0.008 0.001 HIS A 388 PHE 0.008 0.001 PHE A 381 TYR 0.008 0.001 TYR A 363 ARG 0.002 0.000 ARG A 396 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 191) hydrogen bonds : angle 4.13112 ( 549) covalent geometry : bond 0.00342 ( 3351) covalent geometry : angle 0.48360 ( 4561) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.347 Fit side-chains REVERT: A 193 GLN cc_start: 0.9245 (tp-100) cc_final: 0.8806 (tp-100) REVERT: A 230 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7354 (mm) outliers start: 6 outliers final: 3 residues processed: 51 average time/residue: 0.1337 time to fit residues: 8.8477 Evaluate side-chains 49 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 291 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 29 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.153687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.129672 restraints weight = 7319.956| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.97 r_work: 0.3692 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3351 Z= 0.117 Angle : 0.467 5.712 4561 Z= 0.242 Chirality : 0.041 0.127 501 Planarity : 0.004 0.052 579 Dihedral : 6.974 53.821 517 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.82 % Allowed : 13.94 % Favored : 84.24 % 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: 1.74 (0.43), residues: 414 helix: 2.37 (0.34), residues: 209 sheet: -0.18 (0.67), residues: 71 loop : 0.04 (0.59), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 63 HIS 0.009 0.002 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.019 0.001 TYR A 250 ARG 0.001 0.000 ARG A 396 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 191) hydrogen bonds : angle 4.06715 ( 549) covalent geometry : bond 0.00262 ( 3351) covalent geometry : angle 0.46685 ( 4561) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.398 Fit side-chains REVERT: A 193 GLN cc_start: 0.9224 (tp-100) cc_final: 0.8767 (tp-100) REVERT: A 230 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7383 (mm) outliers start: 6 outliers final: 4 residues processed: 49 average time/residue: 0.1099 time to fit residues: 7.3552 Evaluate side-chains 49 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 401 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.149964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.125684 restraints weight = 7115.897| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.87 r_work: 0.3638 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3351 Z= 0.180 Angle : 0.518 5.333 4561 Z= 0.270 Chirality : 0.042 0.125 501 Planarity : 0.004 0.052 579 Dihedral : 6.797 50.639 517 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.82 % Allowed : 14.55 % Favored : 83.64 % 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: 1.52 (0.43), residues: 414 helix: 2.25 (0.34), residues: 206 sheet: -0.31 (0.68), residues: 71 loop : -0.09 (0.58), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 30 HIS 0.008 0.001 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.009 0.001 TYR A 363 ARG 0.002 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 191) hydrogen bonds : angle 4.24993 ( 549) covalent geometry : bond 0.00411 ( 3351) covalent geometry : angle 0.51822 ( 4561) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.364 Fit side-chains REVERT: A 93 LYS cc_start: 0.8475 (ttmt) cc_final: 0.8269 (ttmt) REVERT: A 193 GLN cc_start: 0.9220 (tp-100) cc_final: 0.8794 (tp-100) REVERT: A 230 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7468 (mm) outliers start: 6 outliers final: 5 residues processed: 50 average time/residue: 0.1405 time to fit residues: 9.2842 Evaluate side-chains 49 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 401 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.151433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.127186 restraints weight = 7171.377| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.91 r_work: 0.3664 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3351 Z= 0.137 Angle : 0.497 8.727 4561 Z= 0.253 Chirality : 0.042 0.124 501 Planarity : 0.004 0.053 579 Dihedral : 6.588 48.824 517 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.42 % Allowed : 14.24 % Favored : 83.33 % 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: 1.64 (0.43), residues: 414 helix: 2.32 (0.34), residues: 207 sheet: -0.25 (0.69), residues: 71 loop : -0.02 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 30 HIS 0.008 0.002 HIS A 388 PHE 0.012 0.001 PHE A 381 TYR 0.020 0.001 TYR A 250 ARG 0.001 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.03386 ( 191) hydrogen bonds : angle 4.17526 ( 549) covalent geometry : bond 0.00312 ( 3351) covalent geometry : angle 0.49665 ( 4561) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.370 Fit side-chains REVERT: A 93 LYS cc_start: 0.8395 (ttmt) cc_final: 0.8185 (ttmt) REVERT: A 193 GLN cc_start: 0.9225 (tp-100) cc_final: 0.8796 (tp-100) REVERT: A 230 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7467 (mm) outliers start: 8 outliers final: 6 residues processed: 51 average time/residue: 0.1181 time to fit residues: 8.0632 Evaluate side-chains 51 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 401 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.153503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.129916 restraints weight = 7155.263| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.91 r_work: 0.3692 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3351 Z= 0.110 Angle : 0.474 8.632 4561 Z= 0.243 Chirality : 0.042 0.125 501 Planarity : 0.004 0.053 579 Dihedral : 6.364 46.934 517 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.12 % Allowed : 14.85 % Favored : 83.03 % 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: 1.81 (0.44), residues: 414 helix: 2.39 (0.34), residues: 209 sheet: -0.15 (0.70), residues: 71 loop : 0.14 (0.60), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 63 HIS 0.007 0.001 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.007 0.001 TYR A 132 ARG 0.001 0.000 ARG A 396 Details of bonding type rmsd hydrogen bonds : bond 0.03170 ( 191) hydrogen bonds : angle 4.09024 ( 549) covalent geometry : bond 0.00246 ( 3351) covalent geometry : angle 0.47420 ( 4561) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.383 Fit side-chains REVERT: A 193 GLN cc_start: 0.9228 (tp-100) cc_final: 0.8768 (tp-100) REVERT: A 230 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7443 (mm) outliers start: 7 outliers final: 4 residues processed: 53 average time/residue: 0.1124 time to fit residues: 7.9720 Evaluate side-chains 49 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 291 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.152079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.128071 restraints weight = 7029.979| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.85 r_work: 0.3670 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3351 Z= 0.139 Angle : 0.497 8.449 4561 Z= 0.254 Chirality : 0.042 0.123 501 Planarity : 0.004 0.053 579 Dihedral : 6.313 48.201 517 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.82 % Allowed : 15.15 % Favored : 83.03 % 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: 1.76 (0.44), residues: 414 helix: 2.34 (0.34), residues: 209 sheet: -0.14 (0.70), residues: 71 loop : 0.11 (0.59), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 30 HIS 0.006 0.001 HIS A 388 PHE 0.013 0.001 PHE A 381 TYR 0.020 0.001 TYR A 250 ARG 0.001 0.000 ARG A 370 Details of bonding type rmsd hydrogen bonds : bond 0.03321 ( 191) hydrogen bonds : angle 4.12815 ( 549) covalent geometry : bond 0.00318 ( 3351) covalent geometry : angle 0.49709 ( 4561) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.349 Fit side-chains REVERT: A 193 GLN cc_start: 0.9230 (tp-100) cc_final: 0.8774 (tp-100) REVERT: A 230 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7399 (mm) outliers start: 6 outliers final: 5 residues processed: 49 average time/residue: 0.1229 time to fit residues: 8.0180 Evaluate side-chains 48 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 291 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.0040 chunk 36 optimal weight: 0.0770 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.5752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.154759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.131184 restraints weight = 7104.638| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.90 r_work: 0.3716 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3351 Z= 0.100 Angle : 0.481 8.345 4561 Z= 0.243 Chirality : 0.042 0.127 501 Planarity : 0.004 0.053 579 Dihedral : 6.183 50.718 517 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.82 % Allowed : 14.85 % Favored : 83.33 % 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: 1.87 (0.44), residues: 414 helix: 2.42 (0.35), residues: 211 sheet: -0.15 (0.70), residues: 71 loop : 0.19 (0.60), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 92 HIS 0.006 0.001 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.007 0.001 TYR A 132 ARG 0.002 0.000 ARG A 396 Details of bonding type rmsd hydrogen bonds : bond 0.03054 ( 191) hydrogen bonds : angle 4.07081 ( 549) covalent geometry : bond 0.00220 ( 3351) covalent geometry : angle 0.48082 ( 4561) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1995.74 seconds wall clock time: 34 minutes 52.53 seconds (2092.53 seconds total)