Starting phenix.real_space_refine on Wed Mar 5 20:30:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hho_34805/03_2025/8hho_34805_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hho_34805/03_2025/8hho_34805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hho_34805/03_2025/8hho_34805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hho_34805/03_2025/8hho_34805.map" model { file = "/net/cci-nas-00/data/ceres_data/8hho_34805/03_2025/8hho_34805_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hho_34805/03_2025/8hho_34805_neut.cif" } resolution = 3.2 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-5624/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: 3.02, per 1000 atoms: 0.92 Number of scatterers: 3274 At special positions: 0 Unit cell: (67.048, 72.964, 71.978, 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: 0.81 Conformation dependent library (CDL) restraints added in 377.2 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: 17 helices and 2 sheets defined 55.0% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 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 97 removed outlier: 3.730A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.928A 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 235 Processing helix chain 'A' and resid 256 through 268 removed outlier: 3.653A pdb=" N VAL A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 305 through 309 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 345 through 361 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: 4.451A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLY A 71 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE A 108 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA A 143 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY A 70 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 279 removed outlier: 6.213A pdb=" N ILE A 215 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 241 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 243 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL A 314 " --> pdb=" O ILE A 338 " (cutoff:3.500A) 182 hydrogen bonds defined for protein. 525 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: 0.87 Time building geometry restraints manager: 0.98 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: 1047 1.34 - 1.45: 426 1.45 - 1.57: 1846 1.57 - 1.69: 5 1.69 - 1.80: 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 1.611 0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C4A NAP A 501 " pdb=" C5A NAP A 501 " ideal model delta sigma weight residual 1.385 1.471 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C5A NAP A 501 " pdb=" C6A NAP A 501 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C8A NAP A 501 " pdb=" N7A NAP A 501 " ideal model delta sigma weight residual 1.301 1.359 -0.058 2.00e-02 2.50e+03 8.27e+00 bond pdb=" C1D NAP A 501 " pdb=" O4D NAP A 501 " ideal model delta sigma weight residual 1.375 1.430 -0.055 2.00e-02 2.50e+03 7.61e+00 ... (remaining 3346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 4399 1.81 - 3.61: 131 3.61 - 5.42: 23 5.42 - 7.22: 5 7.22 - 9.03: 3 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 122.40 127.84 -5.44 1.45e+00 4.76e-01 1.41e+01 angle pdb=" N GLY A 70 " pdb=" CA GLY A 70 " pdb=" C GLY A 70 " ideal model delta sigma weight residual 110.87 116.17 -5.30 1.54e+00 4.22e-01 1.19e+01 angle pdb=" C2A NAP A 501 " pdb=" N3A NAP A 501 " pdb=" C4A NAP A 501 " ideal model delta sigma weight residual 111.82 120.85 -9.03 3.00e+00 1.11e-01 9.06e+00 angle pdb=" CA GLU A 233 " pdb=" CB GLU A 233 " pdb=" CG GLU A 233 " ideal model delta sigma weight residual 114.10 119.49 -5.39 2.00e+00 2.50e-01 7.25e+00 angle pdb=" PA NAP A 501 " pdb=" O3 NAP A 501 " pdb=" PN NAP A 501 " ideal model delta sigma weight residual 128.45 120.55 7.90 3.00e+00 1.11e-01 6.93e+00 ... (remaining 4556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 1792 17.95 - 35.90: 179 35.90 - 53.84: 53 53.84 - 71.79: 3 71.79 - 89.74: 5 Dihedral angle restraints: 2032 sinusoidal: 843 harmonic: 1189 Sorted by residual: dihedral pdb=" CA MET A 153 " pdb=" C MET A 153 " pdb=" N GLY A 154 " pdb=" CA GLY A 154 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 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 180.00 162.34 17.66 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CB GLU A 316 " pdb=" CG GLU A 316 " pdb=" CD GLU A 316 " pdb=" OE1 GLU A 316 " ideal model delta sinusoidal sigma weight residual 0.00 89.74 -89.74 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 2029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 370 0.044 - 0.088: 89 0.088 - 0.132: 38 0.132 - 0.176: 1 0.176 - 0.220: 3 Chirality restraints: 501 Sorted by residual: chirality pdb=" C2B NAP A 501 " pdb=" C1B NAP A 501 " pdb=" C3B NAP A 501 " pdb=" O2B NAP A 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.54 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C1B NAP A 501 " pdb=" C2B NAP A 501 " pdb=" N9A NAP A 501 " pdb=" O4B NAP A 501 " both_signs ideal model delta sigma weight residual False 2.31 2.52 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C3D NAP A 501 " pdb=" C2D NAP A 501 " pdb=" C4D NAP A 501 " pdb=" O3D NAP A 501 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.20 2.00e-01 2.50e+01 9.62e-01 ... (remaining 498 not shown) Planarity restraints: 579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 75 " -0.032 5.00e-02 4.00e+02 4.95e-02 3.91e+00 pdb=" N PRO A 76 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO A 142 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 396 " -0.129 9.50e-02 1.11e+02 5.82e-02 2.33e+00 pdb=" NE ARG A 396 " 0.005 2.00e-02 2.50e+03 pdb=" CZ ARG A 396 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 396 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 396 " -0.008 2.00e-02 2.50e+03 ... (remaining 576 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 133 2.72 - 3.26: 3421 3.26 - 3.81: 5773 3.81 - 4.35: 7046 4.35 - 4.90: 11574 Nonbonded interactions: 27947 Sorted by model distance: nonbonded pdb=" O2N NAP A 501 " pdb=" O3D NAP A 501 " model vdw 2.169 3.040 nonbonded pdb=" NH2 ARG A 65 " pdb=" OD1 ASP A 98 " model vdw 2.268 3.120 nonbonded pdb=" ND2 ASN A 251 " pdb=" O GLY A 275 " model vdw 2.268 3.120 nonbonded pdb=" ND1 HIS A 388 " pdb=" O ILE A 393 " model vdw 2.295 3.120 nonbonded pdb=" NZ LYS A 105 " pdb=" OD2 ASP A 145 " model vdw 2.310 3.120 ... (remaining 27942 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.200 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 : 0.005 0.125 3351 Z= 0.314 Angle : 0.764 9.028 4561 Z= 0.415 Chirality : 0.045 0.220 501 Planarity : 0.005 0.058 579 Dihedral : 15.654 89.740 1274 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.30 % Allowed : 0.61 % 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: 1.56 (0.42), residues: 414 helix: 1.92 (0.37), residues: 210 sheet: 0.99 (0.69), residues: 61 loop : -0.23 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 92 HIS 0.006 0.002 HIS A 388 PHE 0.004 0.001 PHE A 381 TYR 0.018 0.001 TYR A 385 ARG 0.009 0.000 ARG A 396 *********************** 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 74 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.394 Fit side-chains REVERT: A 385 TYR cc_start: 0.7648 (t80) cc_final: 0.7294 (t80) outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.1850 time to fit residues: 16.3443 Evaluate side-chains 62 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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: 0.7980 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN A 392 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.138905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.118251 restraints weight = 7026.671| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.68 r_work: 0.3493 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3351 Z= 0.212 Angle : 0.570 5.656 4561 Z= 0.300 Chirality : 0.045 0.149 501 Planarity : 0.005 0.040 579 Dihedral : 9.868 88.380 517 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.52 % Allowed : 10.00 % Favored : 88.48 % 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: 1.67 (0.42), residues: 414 helix: 2.12 (0.35), residues: 208 sheet: 0.98 (0.70), residues: 61 loop : -0.29 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 263 HIS 0.005 0.002 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.022 0.002 TYR A 250 ARG 0.004 0.000 ARG A 65 *********************** 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 76 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 ARG cc_start: 0.8958 (ttp-170) cc_final: 0.8735 (ttp-170) REVERT: A 249 ILE cc_start: 0.7535 (mm) cc_final: 0.7075 (mt) REVERT: A 263 TRP cc_start: 0.7846 (t-100) cc_final: 0.7504 (t-100) REVERT: A 366 GLU cc_start: 0.8605 (pm20) cc_final: 0.8382 (pm20) outliers start: 5 outliers final: 2 residues processed: 73 average time/residue: 0.1751 time to fit residues: 15.3369 Evaluate side-chains 68 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 226 TYR 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: 1.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.135991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.115661 restraints weight = 6837.076| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.52 r_work: 0.3451 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3351 Z= 0.286 Angle : 0.597 8.739 4561 Z= 0.312 Chirality : 0.046 0.171 501 Planarity : 0.005 0.042 579 Dihedral : 9.061 83.235 517 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.21 % Allowed : 13.64 % Favored : 85.15 % 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: 1.46 (0.42), residues: 414 helix: 1.93 (0.35), residues: 208 sheet: 0.76 (0.70), residues: 61 loop : -0.31 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 92 HIS 0.005 0.002 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.022 0.002 TYR A 250 ARG 0.003 0.000 ARG A 65 *********************** 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 75 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 200 ARG cc_start: 0.8974 (ttp-170) cc_final: 0.8755 (ttp-170) REVERT: A 249 ILE cc_start: 0.7517 (mm) cc_final: 0.6994 (mt) REVERT: A 263 TRP cc_start: 0.7800 (t-100) cc_final: 0.7450 (t-100) outliers start: 4 outliers final: 2 residues processed: 73 average time/residue: 0.1722 time to fit residues: 15.2275 Evaluate side-chains 66 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 314 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 38 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.138282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.117855 restraints weight = 6986.257| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.63 r_work: 0.3478 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3351 Z= 0.178 Angle : 0.533 5.667 4561 Z= 0.285 Chirality : 0.044 0.153 501 Planarity : 0.005 0.041 579 Dihedral : 8.508 81.943 517 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.21 % Allowed : 14.85 % Favored : 83.94 % 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: 1.66 (0.42), residues: 414 helix: 2.08 (0.36), residues: 202 sheet: 0.83 (0.68), residues: 66 loop : -0.11 (0.53), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 92 HIS 0.005 0.002 HIS A 388 PHE 0.009 0.001 PHE A 57 TYR 0.023 0.002 TYR A 250 ARG 0.001 0.000 ARG A 396 *********************** 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 81 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 ASN cc_start: 0.8684 (t0) cc_final: 0.8382 (t0) REVERT: A 263 TRP cc_start: 0.7811 (t-100) cc_final: 0.7442 (t-100) REVERT: A 367 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7955 (mm-30) outliers start: 4 outliers final: 2 residues processed: 80 average time/residue: 0.1779 time to fit residues: 17.0425 Evaluate side-chains 69 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 314 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 0.0670 chunk 5 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.138928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.118391 restraints weight = 6971.776| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.65 r_work: 0.3491 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3351 Z= 0.175 Angle : 0.557 6.368 4561 Z= 0.289 Chirality : 0.044 0.152 501 Planarity : 0.005 0.040 579 Dihedral : 8.011 80.000 517 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.12 % Allowed : 16.36 % Favored : 81.52 % 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: 1.72 (0.42), residues: 414 helix: 2.11 (0.36), residues: 202 sheet: 0.97 (0.68), residues: 66 loop : -0.10 (0.53), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 92 HIS 0.006 0.002 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.025 0.001 TYR A 250 ARG 0.002 0.000 ARG A 396 *********************** 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 74 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 ASN cc_start: 0.8625 (t0) cc_final: 0.8256 (t0) REVERT: A 263 TRP cc_start: 0.7856 (t-100) cc_final: 0.7645 (t-100) outliers start: 7 outliers final: 6 residues processed: 71 average time/residue: 0.1470 time to fit residues: 12.8903 Evaluate side-chains 70 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 314 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.138595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.118003 restraints weight = 7130.255| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.69 r_work: 0.3478 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 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 : 0.003 0.036 3351 Z= 0.188 Angle : 0.547 5.970 4561 Z= 0.286 Chirality : 0.044 0.159 501 Planarity : 0.004 0.040 579 Dihedral : 7.744 80.844 517 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.52 % Allowed : 16.06 % Favored : 82.42 % 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: 1.76 (0.42), residues: 414 helix: 2.14 (0.36), residues: 202 sheet: 0.95 (0.68), residues: 66 loop : -0.07 (0.53), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 263 HIS 0.005 0.002 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.025 0.001 TYR A 250 ARG 0.003 0.000 ARG A 396 *********************** 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 75 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASN cc_start: 0.8606 (t0) cc_final: 0.8232 (t0) REVERT: A 263 TRP cc_start: 0.7923 (t-100) cc_final: 0.7693 (t-100) REVERT: A 283 GLU cc_start: 0.8363 (tt0) cc_final: 0.7888 (tp30) REVERT: A 367 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7825 (mm-30) outliers start: 5 outliers final: 4 residues processed: 72 average time/residue: 0.1714 time to fit residues: 15.1090 Evaluate side-chains 71 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 314 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.136694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.116368 restraints weight = 6903.114| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.53 r_work: 0.3457 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3351 Z= 0.241 Angle : 0.570 7.157 4561 Z= 0.298 Chirality : 0.044 0.166 501 Planarity : 0.005 0.041 579 Dihedral : 7.829 82.660 517 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.42 % Allowed : 15.76 % 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: 1.63 (0.42), residues: 414 helix: 2.12 (0.36), residues: 202 sheet: 0.75 (0.67), residues: 66 loop : -0.20 (0.52), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 263 HIS 0.005 0.002 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.026 0.002 TYR A 250 ARG 0.004 0.000 ARG A 396 *********************** 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 78 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASN cc_start: 0.8614 (t0) cc_final: 0.8224 (t0) REVERT: A 263 TRP cc_start: 0.7807 (t-100) cc_final: 0.7581 (t-100) REVERT: A 283 GLU cc_start: 0.8347 (tt0) cc_final: 0.7968 (tp30) REVERT: A 367 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8102 (mm-30) outliers start: 8 outliers final: 6 residues processed: 74 average time/residue: 0.1563 time to fit residues: 14.2993 Evaluate side-chains 71 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 314 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 40 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 23 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.137358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.117128 restraints weight = 6995.424| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.57 r_work: 0.3473 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3351 Z= 0.208 Angle : 0.566 6.446 4561 Z= 0.297 Chirality : 0.044 0.174 501 Planarity : 0.005 0.042 579 Dihedral : 7.717 82.071 517 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.12 % Allowed : 17.88 % Favored : 80.00 % 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: 1.60 (0.42), residues: 414 helix: 2.09 (0.36), residues: 202 sheet: 0.78 (0.67), residues: 66 loop : -0.22 (0.52), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 263 HIS 0.006 0.002 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.026 0.002 TYR A 250 ARG 0.003 0.000 ARG A 396 *********************** 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 76 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 ASN cc_start: 0.8622 (t0) cc_final: 0.8238 (t0) REVERT: A 263 TRP cc_start: 0.7832 (t-100) cc_final: 0.7611 (t-100) REVERT: A 283 GLU cc_start: 0.8369 (tt0) cc_final: 0.7967 (tp30) REVERT: A 367 GLU cc_start: 0.8245 (mm-30) cc_final: 0.8040 (mm-30) outliers start: 7 outliers final: 6 residues processed: 73 average time/residue: 0.1600 time to fit residues: 14.2375 Evaluate side-chains 72 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 314 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.137304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.117005 restraints weight = 6986.989| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.53 r_work: 0.3468 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3351 Z= 0.211 Angle : 0.569 7.980 4561 Z= 0.300 Chirality : 0.044 0.178 501 Planarity : 0.005 0.042 579 Dihedral : 7.699 82.348 517 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.82 % Allowed : 18.18 % Favored : 80.00 % 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: 1.56 (0.42), residues: 414 helix: 2.05 (0.36), residues: 202 sheet: 0.77 (0.67), residues: 66 loop : -0.23 (0.52), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 92 HIS 0.007 0.002 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.026 0.002 TYR A 250 ARG 0.003 0.000 ARG A 396 *********************** 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 75 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 ASN cc_start: 0.8574 (t0) cc_final: 0.8238 (t0) REVERT: A 263 TRP cc_start: 0.7793 (t-100) cc_final: 0.7563 (t-100) REVERT: A 283 GLU cc_start: 0.8295 (tt0) cc_final: 0.8045 (tp30) REVERT: A 396 ARG cc_start: 0.7615 (mtm180) cc_final: 0.7104 (mtm180) outliers start: 6 outliers final: 6 residues processed: 73 average time/residue: 0.1580 time to fit residues: 14.1656 Evaluate side-chains 74 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 314 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 chunk 39 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 0.1980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.140032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.120254 restraints weight = 6776.289| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.52 r_work: 0.3517 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3351 Z= 0.177 Angle : 0.556 7.808 4561 Z= 0.294 Chirality : 0.044 0.159 501 Planarity : 0.005 0.042 579 Dihedral : 7.546 81.337 517 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.82 % Allowed : 18.79 % Favored : 79.39 % 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: 1.65 (0.42), residues: 414 helix: 2.07 (0.36), residues: 202 sheet: 0.90 (0.68), residues: 66 loop : -0.16 (0.52), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 92 HIS 0.007 0.002 HIS A 388 PHE 0.012 0.001 PHE A 381 TYR 0.024 0.001 TYR A 250 ARG 0.002 0.000 ARG A 396 ********************** 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 77 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 ASN cc_start: 0.8554 (t0) cc_final: 0.8158 (t0) REVERT: A 263 TRP cc_start: 0.7860 (t-100) cc_final: 0.7638 (t-100) REVERT: A 396 ARG cc_start: 0.7558 (mtm180) cc_final: 0.7325 (mtm180) outliers start: 6 outliers final: 6 residues processed: 75 average time/residue: 0.1631 time to fit residues: 14.9324 Evaluate side-chains 73 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 314 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 0.0060 chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 39 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.139868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.120028 restraints weight = 6829.731| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.55 r_work: 0.3510 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3351 Z= 0.189 Angle : 0.569 7.536 4561 Z= 0.299 Chirality : 0.044 0.164 501 Planarity : 0.005 0.041 579 Dihedral : 7.537 81.595 517 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.12 % Allowed : 18.18 % Favored : 79.70 % 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: 1.64 (0.42), residues: 414 helix: 2.07 (0.36), residues: 202 sheet: 0.90 (0.67), residues: 66 loop : -0.18 (0.53), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 92 HIS 0.007 0.002 HIS A 388 PHE 0.015 0.001 PHE A 381 TYR 0.023 0.001 TYR A 250 ARG 0.002 0.000 ARG A 396 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1815.14 seconds wall clock time: 32 minutes 3.85 seconds (1923.85 seconds total)