Starting phenix.real_space_refine on Fri May 9 13:03:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9arx_43797/05_2025/9arx_43797.cif Found real_map, /net/cci-nas-00/data/ceres_data/9arx_43797/05_2025/9arx_43797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9arx_43797/05_2025/9arx_43797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9arx_43797/05_2025/9arx_43797.map" model { file = "/net/cci-nas-00/data/ceres_data/9arx_43797/05_2025/9arx_43797.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9arx_43797/05_2025/9arx_43797.cif" } resolution = 3.24 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= 0.018 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: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1234 2.51 5 N 291 2.21 5 O 314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 1851 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1838 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 80 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.37, per 1000 atoms: 1.28 Number of scatterers: 1851 At special positions: 0 Unit cell: (62.48, 69.52, 64.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 314 8.00 N 291 7.00 C 1234 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 227 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 246.4 milliseconds 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 492 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 91.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 80 through 102 removed outlier: 3.876A pdb=" N VAL A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 106 removed outlier: 3.689A pdb=" N GLN A 106 " --> pdb=" O LYS A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 107 through 127 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 147 through 179 removed outlier: 3.513A pdb=" N TRP A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 186 removed outlier: 3.615A pdb=" N PHE A 186 " --> pdb=" O HIS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 207 removed outlier: 4.091A pdb=" N ALA A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 removed outlier: 4.440A pdb=" N VAL A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 213 " --> pdb=" O PRO A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 213' Processing helix chain 'A' and resid 217 through 221 removed outlier: 3.655A pdb=" N LYS A 220 " --> pdb=" O ASP A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 243 removed outlier: 3.892A pdb=" N ILE A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 261 removed outlier: 3.856A pdb=" N ILE A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 349 removed outlier: 3.622A pdb=" N GLN A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) Proline residue: A 338 - end of helix removed outlier: 3.596A pdb=" N VAL A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 382 removed outlier: 3.826A pdb=" N VAL A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TRP A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA A 374 " --> pdb=" O TYR A 370 " (cutoff:3.500A) Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.761A pdb=" N ARG A 388 " --> pdb=" O ASN A 384 " (cutoff:3.500A) 149 hydrogen bonds defined for protein. 444 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: 0.48 Time building geometry restraints manager: 0.60 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: 546 1.34 - 1.46: 331 1.46 - 1.58: 999 1.58 - 1.69: 1 1.69 - 1.81: 18 Bond restraints: 1895 Sorted by residual: bond pdb=" CD2 SRO A 501 " pdb=" CE2 SRO A 501 " ideal model delta sigma weight residual 1.419 1.367 0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" CD1 SRO A 501 " pdb=" NE1 SRO A 501 " ideal model delta sigma weight residual 1.377 1.327 0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" C ILE A 210 " pdb=" N PRO A 211 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.42e+00 bond pdb=" CB PRO A 144 " pdb=" CG PRO A 144 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.01e+00 bond pdb=" C ILE A 245 " pdb=" N PRO A 246 " ideal model delta sigma weight residual 1.335 1.355 -0.021 1.28e-02 6.10e+03 2.62e+00 ... (remaining 1890 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 2431 1.49 - 2.99: 138 2.99 - 4.48: 21 4.48 - 5.97: 8 5.97 - 7.46: 6 Bond angle restraints: 2604 Sorted by residual: angle pdb=" CA PRO A 144 " pdb=" N PRO A 144 " pdb=" CD PRO A 144 " ideal model delta sigma weight residual 112.00 105.29 6.71 1.40e+00 5.10e-01 2.30e+01 angle pdb=" N CYS A 337 " pdb=" CA CYS A 337 " pdb=" C CYS A 337 " ideal model delta sigma weight residual 109.81 116.95 -7.14 2.21e+00 2.05e-01 1.04e+01 angle pdb=" CA CYS A 337 " pdb=" C CYS A 337 " pdb=" N PRO A 338 " ideal model delta sigma weight residual 118.44 123.09 -4.65 1.59e+00 3.96e-01 8.55e+00 angle pdb=" CA ASN A 187 " pdb=" C ASN A 187 " pdb=" N SER A 188 " ideal model delta sigma weight residual 114.76 117.92 -3.16 1.14e+00 7.69e-01 7.66e+00 angle pdb=" N ASN A 187 " pdb=" CA ASN A 187 " pdb=" C ASN A 187 " ideal model delta sigma weight residual 109.39 113.64 -4.25 1.59e+00 3.96e-01 7.13e+00 ... (remaining 2599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 963 16.89 - 33.79: 99 33.79 - 50.68: 16 50.68 - 67.57: 4 67.57 - 84.46: 2 Dihedral angle restraints: 1084 sinusoidal: 332 harmonic: 752 Sorted by residual: dihedral pdb=" CB CYS A 148 " pdb=" SG CYS A 148 " pdb=" SG CYS A 227 " pdb=" CB CYS A 227 " ideal model delta sinusoidal sigma weight residual -86.00 -170.46 84.46 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CA PRO A 144 " pdb=" C PRO A 144 " pdb=" N SER A 145 " pdb=" CA SER A 145 " ideal model delta harmonic sigma weight residual 180.00 -160.49 -19.51 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ARG A 140 " pdb=" C ARG A 140 " pdb=" N TRP A 141 " pdb=" CA TRP A 141 " ideal model delta harmonic sigma weight residual -180.00 -161.80 -18.20 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 1081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 223 0.044 - 0.088: 86 0.088 - 0.132: 16 0.132 - 0.176: 6 0.176 - 0.220: 1 Chirality restraints: 332 Sorted by residual: chirality pdb=" CB VAL A 241 " pdb=" CA VAL A 241 " pdb=" CG1 VAL A 241 " pdb=" CG2 VAL A 241 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA CYS A 337 " pdb=" N CYS A 337 " pdb=" C CYS A 337 " pdb=" CB CYS A 337 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA MET A 208 " pdb=" N MET A 208 " pdb=" C MET A 208 " pdb=" CB MET A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.39e-01 ... (remaining 329 not shown) Planarity restraints: 313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 143 " -0.049 5.00e-02 4.00e+02 7.10e-02 8.06e+00 pdb=" N PRO A 144 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 337 " -0.038 5.00e-02 4.00e+02 5.65e-02 5.10e+00 pdb=" N PRO A 338 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 338 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 338 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 245 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.69e+00 pdb=" N PRO A 246 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 246 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 246 " -0.031 5.00e-02 4.00e+02 ... (remaining 310 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 577 2.82 - 3.34: 1744 3.34 - 3.86: 3039 3.86 - 4.38: 3318 4.38 - 4.90: 6009 Nonbonded interactions: 14687 Sorted by model distance: nonbonded pdb=" OD2 ASP A 155 " pdb=" OH TYR A 370 " model vdw 2.302 3.040 nonbonded pdb=" OD1 ASN A 110 " pdb=" OH TYR A 387 " model vdw 2.306 3.040 nonbonded pdb=" O THR A 253 " pdb=" OG1 THR A 257 " model vdw 2.347 3.040 nonbonded pdb=" O ALA A 161 " pdb=" ND1 HIS A 165 " model vdw 2.364 3.120 nonbonded pdb=" O VAL A 199 " pdb=" OG SER A 203 " model vdw 2.365 3.040 ... (remaining 14682 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: 1.470 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.750 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 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 : 0.006 0.087 1896 Z= 0.249 Angle : 0.858 7.463 2606 Z= 0.497 Chirality : 0.049 0.220 332 Planarity : 0.009 0.071 313 Dihedral : 14.131 72.776 589 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 18.64 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.46), residues: 250 helix: -1.11 (0.30), residues: 205 sheet: None (None), residues: 0 loop : -1.54 (0.95), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 141 HIS 0.005 0.002 HIS A 165 PHE 0.015 0.002 PHE A 244 TYR 0.010 0.001 TYR A 153 ARG 0.001 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.14034 ( 149) hydrogen bonds : angle 6.19686 ( 444) SS BOND : bond 0.00151 ( 1) SS BOND : angle 0.97840 ( 2) covalent geometry : bond 0.00557 ( 1895) covalent geometry : angle 0.85769 ( 2604) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.207 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1063 time to fit residues: 4.3470 Evaluate side-chains 30 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.157822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.143449 restraints weight = 2382.932| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.40 r_work: 0.3600 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1896 Z= 0.156 Angle : 0.548 5.007 2606 Z= 0.286 Chirality : 0.039 0.106 332 Planarity : 0.005 0.039 313 Dihedral : 4.816 27.560 266 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.95 % Allowed : 15.82 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.53), residues: 250 helix: 0.28 (0.35), residues: 206 sheet: None (None), residues: 0 loop : -0.95 (1.13), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 141 HIS 0.005 0.002 HIS A 165 PHE 0.012 0.001 PHE A 244 TYR 0.009 0.001 TYR A 174 ARG 0.000 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.04046 ( 149) hydrogen bonds : angle 4.09217 ( 444) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.30697 ( 2) covalent geometry : bond 0.00365 ( 1895) covalent geometry : angle 0.54814 ( 2604) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.208 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 36 average time/residue: 0.0910 time to fit residues: 4.1479 Evaluate side-chains 31 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 386 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 0.0670 chunk 13 optimal weight: 0.0870 chunk 14 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 overall best weight: 0.3296 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.161201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.147465 restraints weight = 2325.516| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.31 r_work: 0.3644 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 1896 Z= 0.108 Angle : 0.503 6.263 2606 Z= 0.253 Chirality : 0.038 0.099 332 Planarity : 0.004 0.031 313 Dihedral : 5.017 39.185 266 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 3.39 % Allowed : 16.95 % Favored : 79.66 % 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: 1.16 (0.54), residues: 250 helix: 1.11 (0.35), residues: 206 sheet: None (None), residues: 0 loop : -0.56 (1.14), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 141 HIS 0.003 0.001 HIS A 165 PHE 0.012 0.001 PHE A 244 TYR 0.005 0.001 TYR A 174 ARG 0.000 0.000 ARG A 185 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 149) hydrogen bonds : angle 3.76961 ( 444) SS BOND : bond 0.00044 ( 1) SS BOND : angle 0.24844 ( 2) covalent geometry : bond 0.00240 ( 1895) covalent geometry : angle 0.50363 ( 2604) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.204 Fit side-chains REVERT: A 141 TRP cc_start: 0.7185 (OUTLIER) cc_final: 0.5993 (t60) outliers start: 6 outliers final: 4 residues processed: 32 average time/residue: 0.0976 time to fit residues: 3.9907 Evaluate side-chains 33 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 344 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 0.2980 chunk 21 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.160352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.146980 restraints weight = 2313.083| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.28 r_work: 0.3627 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1896 Z= 0.130 Angle : 0.523 5.025 2606 Z= 0.263 Chirality : 0.039 0.104 332 Planarity : 0.004 0.032 313 Dihedral : 4.564 30.777 266 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.65 % Allowed : 14.12 % Favored : 80.23 % 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: 1.44 (0.55), residues: 250 helix: 1.34 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -0.64 (1.12), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 141 HIS 0.003 0.001 HIS A 165 PHE 0.012 0.001 PHE A 244 TYR 0.007 0.001 TYR A 174 ARG 0.000 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.03552 ( 149) hydrogen bonds : angle 3.78980 ( 444) SS BOND : bond 0.00133 ( 1) SS BOND : angle 0.41604 ( 2) covalent geometry : bond 0.00306 ( 1895) covalent geometry : angle 0.52327 ( 2604) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.221 Fit side-chains REVERT: A 141 TRP cc_start: 0.7366 (OUTLIER) cc_final: 0.6299 (t60) outliers start: 10 outliers final: 7 residues processed: 37 average time/residue: 0.0900 time to fit residues: 4.2073 Evaluate side-chains 34 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 316 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 0.0050 chunk 7 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 0.0370 chunk 12 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.3472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.161356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.147726 restraints weight = 2356.115| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.31 r_work: 0.3651 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 1896 Z= 0.107 Angle : 0.490 5.035 2606 Z= 0.247 Chirality : 0.038 0.102 332 Planarity : 0.003 0.029 313 Dihedral : 4.785 37.734 266 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 5.08 % Allowed : 16.38 % Favored : 78.53 % 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 (0.55), residues: 250 helix: 1.62 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -0.61 (1.14), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 141 HIS 0.003 0.001 HIS A 165 PHE 0.012 0.001 PHE A 244 TYR 0.005 0.001 TYR A 174 ARG 0.000 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.03188 ( 149) hydrogen bonds : angle 3.66510 ( 444) SS BOND : bond 0.00056 ( 1) SS BOND : angle 0.37250 ( 2) covalent geometry : bond 0.00243 ( 1895) covalent geometry : angle 0.49003 ( 2604) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.209 Fit side-chains REVERT: A 141 TRP cc_start: 0.7285 (OUTLIER) cc_final: 0.6263 (t60) outliers start: 9 outliers final: 7 residues processed: 37 average time/residue: 0.0928 time to fit residues: 4.3403 Evaluate side-chains 36 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 316 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 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 = 0.3802 r_free = 0.3802 target = 0.156399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.142998 restraints weight = 2370.819| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.30 r_work: 0.3592 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1896 Z= 0.159 Angle : 0.543 5.154 2606 Z= 0.275 Chirality : 0.040 0.111 332 Planarity : 0.004 0.032 313 Dihedral : 4.451 26.328 266 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.08 % Allowed : 16.38 % Favored : 78.53 % 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: 1.53 (0.55), residues: 250 helix: 1.41 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -0.63 (1.15), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 141 HIS 0.004 0.001 HIS A 165 PHE 0.011 0.001 PHE A 244 TYR 0.007 0.001 TYR A 174 ARG 0.000 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 149) hydrogen bonds : angle 3.88004 ( 444) SS BOND : bond 0.00142 ( 1) SS BOND : angle 0.57549 ( 2) covalent geometry : bond 0.00382 ( 1895) covalent geometry : angle 0.54293 ( 2604) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.203 Fit side-chains REVERT: A 141 TRP cc_start: 0.7479 (OUTLIER) cc_final: 0.6524 (t60) outliers start: 9 outliers final: 5 residues processed: 35 average time/residue: 0.1027 time to fit residues: 4.4363 Evaluate side-chains 34 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 248 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 0.0050 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.158595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.144991 restraints weight = 2343.551| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.32 r_work: 0.3622 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1896 Z= 0.122 Angle : 0.503 5.095 2606 Z= 0.255 Chirality : 0.038 0.103 332 Planarity : 0.004 0.031 313 Dihedral : 4.659 33.892 266 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.52 % Allowed : 17.51 % Favored : 77.97 % 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: 1.71 (0.55), residues: 250 helix: 1.54 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -0.68 (1.13), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 141 HIS 0.004 0.001 HIS A 165 PHE 0.013 0.001 PHE A 244 TYR 0.006 0.001 TYR A 153 ARG 0.000 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.03438 ( 149) hydrogen bonds : angle 3.80106 ( 444) SS BOND : bond 0.00098 ( 1) SS BOND : angle 0.47832 ( 2) covalent geometry : bond 0.00284 ( 1895) covalent geometry : angle 0.50308 ( 2604) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.195 Fit side-chains REVERT: A 141 TRP cc_start: 0.7381 (OUTLIER) cc_final: 0.6469 (t60) outliers start: 8 outliers final: 6 residues processed: 35 average time/residue: 0.0965 time to fit residues: 4.2371 Evaluate side-chains 33 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 0.0980 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.158007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.144543 restraints weight = 2356.689| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.30 r_work: 0.3615 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1896 Z= 0.130 Angle : 0.510 5.114 2606 Z= 0.259 Chirality : 0.039 0.105 332 Planarity : 0.004 0.031 313 Dihedral : 4.585 31.881 266 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.95 % Allowed : 18.08 % Favored : 77.97 % 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: 1.69 (0.55), residues: 250 helix: 1.54 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -0.72 (1.11), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 141 HIS 0.004 0.001 HIS A 165 PHE 0.012 0.001 PHE A 244 TYR 0.006 0.001 TYR A 174 ARG 0.000 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 149) hydrogen bonds : angle 3.80921 ( 444) SS BOND : bond 0.00156 ( 1) SS BOND : angle 0.50942 ( 2) covalent geometry : bond 0.00307 ( 1895) covalent geometry : angle 0.51005 ( 2604) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.202 Fit side-chains REVERT: A 141 TRP cc_start: 0.7410 (OUTLIER) cc_final: 0.6500 (t60) outliers start: 7 outliers final: 6 residues processed: 35 average time/residue: 0.0890 time to fit residues: 3.9725 Evaluate side-chains 35 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 4 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 23 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.0870 chunk 17 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.160069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.146326 restraints weight = 2393.080| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.33 r_work: 0.3633 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1896 Z= 0.111 Angle : 0.489 5.069 2606 Z= 0.248 Chirality : 0.038 0.107 332 Planarity : 0.003 0.030 313 Dihedral : 4.667 35.627 266 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.52 % Allowed : 17.51 % Favored : 77.97 % 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: 1.85 (0.55), residues: 250 helix: 1.66 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -0.69 (1.11), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 141 HIS 0.004 0.001 HIS A 165 PHE 0.013 0.001 PHE A 244 TYR 0.006 0.001 TYR A 153 ARG 0.000 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.03252 ( 149) hydrogen bonds : angle 3.72530 ( 444) SS BOND : bond 0.00122 ( 1) SS BOND : angle 0.43352 ( 2) covalent geometry : bond 0.00256 ( 1895) covalent geometry : angle 0.48902 ( 2604) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.219 Fit side-chains REVERT: A 141 TRP cc_start: 0.7277 (OUTLIER) cc_final: 0.6450 (t60) outliers start: 8 outliers final: 6 residues processed: 37 average time/residue: 0.1046 time to fit residues: 4.8991 Evaluate side-chains 36 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 0.0870 chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 0.0570 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.160343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.146805 restraints weight = 2340.789| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.30 r_work: 0.3636 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1896 Z= 0.113 Angle : 0.490 5.068 2606 Z= 0.248 Chirality : 0.038 0.114 332 Planarity : 0.003 0.030 313 Dihedral : 4.599 34.418 266 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.95 % Allowed : 18.64 % Favored : 77.40 % 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: 1.92 (0.55), residues: 250 helix: 1.71 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -0.71 (1.11), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 141 HIS 0.004 0.001 HIS A 165 PHE 0.012 0.001 PHE A 244 TYR 0.006 0.001 TYR A 174 ARG 0.000 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 149) hydrogen bonds : angle 3.71162 ( 444) SS BOND : bond 0.00125 ( 1) SS BOND : angle 0.42886 ( 2) covalent geometry : bond 0.00261 ( 1895) covalent geometry : angle 0.49018 ( 2604) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.196 Fit side-chains REVERT: A 141 TRP cc_start: 0.7267 (OUTLIER) cc_final: 0.6499 (t60) outliers start: 7 outliers final: 6 residues processed: 37 average time/residue: 0.0882 time to fit residues: 4.1257 Evaluate side-chains 37 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 0.0980 chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 6 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 0.0670 chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 overall best weight: 0.2918 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.163269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.149526 restraints weight = 2300.252| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.35 r_work: 0.3656 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 1896 Z= 0.101 Angle : 0.476 5.017 2606 Z= 0.242 Chirality : 0.038 0.112 332 Planarity : 0.003 0.029 313 Dihedral : 4.733 37.895 266 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.95 % Allowed : 18.08 % Favored : 77.97 % 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: 2.10 (0.55), residues: 250 helix: 1.84 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -0.71 (1.12), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 141 HIS 0.003 0.001 HIS A 165 PHE 0.013 0.001 PHE A 244 TYR 0.009 0.001 TYR A 153 ARG 0.000 0.000 ARG A 185 Details of bonding type rmsd hydrogen bonds : bond 0.03042 ( 149) hydrogen bonds : angle 3.67538 ( 444) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.39065 ( 2) covalent geometry : bond 0.00226 ( 1895) covalent geometry : angle 0.47588 ( 2604) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1424.93 seconds wall clock time: 25 minutes 26.33 seconds (1526.33 seconds total)