Starting phenix.real_space_refine on Tue Feb 3 12:37:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p1s_71130/02_2026/9p1s_71130.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p1s_71130/02_2026/9p1s_71130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9p1s_71130/02_2026/9p1s_71130.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p1s_71130/02_2026/9p1s_71130.map" model { file = "/net/cci-nas-00/data/ceres_data/9p1s_71130/02_2026/9p1s_71130.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p1s_71130/02_2026/9p1s_71130.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 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 18 5.16 5 C 1456 2.51 5 N 348 2.21 5 O 357 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2179 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2096 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 271, 2090 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 261} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 271, 2090 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 261} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 2135 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'LMN': 1, 'ZMA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 5 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER A 35 " occ=0.60 ... (10 atoms not shown) pdb=" OG BSER A 35 " occ=0.40 Time building chain proxies: 0.88, per 1000 atoms: 0.40 Number of scatterers: 2179 At special positions: 0 Unit cell: (49.288, 71.104, 63.832, 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 18 16.00 O 357 8.00 N 348 7.00 C 1456 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 146 " distance=2.03 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 166 " 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: 0.25 Conformation dependent library (CDL) restraints added in 159.1 milliseconds 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 520 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 0 sheets defined 88.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 6 through 34 Processing helix chain 'A' and resid 40 through 58 Processing helix chain 'A' and resid 58 through 69 Processing helix chain 'A' and resid 73 through 108 removed outlier: 5.105A pdb=" N VAL A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 86 " --> pdb=" O CYS A 82 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 117 through 137 removed outlier: 3.588A pdb=" N ALA A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 removed outlier: 3.644A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 removed outlier: 3.512A pdb=" N VAL A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 186 through 207 Processing helix chain 'A' and resid 318 through 355 Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 362 through 388 removed outlier: 3.648A pdb=" N ASN A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASN A 380 " --> pdb=" O ASN A 376 " (cutoff:3.500A) Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 388 through 399 171 hydrogen bonds defined for protein. 513 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: 0.21 Time building geometry restraints manager: 0.28 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: 611 1.34 - 1.45: 369 1.45 - 1.57: 1234 1.57 - 1.69: 0 1.69 - 1.81: 23 Bond restraints: 2237 Sorted by residual: bond pdb=" N ILE A 53 " pdb=" CA ILE A 53 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.35e+00 bond pdb=" N ILE A 334 " pdb=" CA ILE A 334 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.30e-02 5.92e+03 7.24e+00 bond pdb=" N VAL A 55 " pdb=" CA VAL A 55 " ideal model delta sigma weight residual 1.461 1.493 -0.031 1.17e-02 7.31e+03 7.11e+00 bond pdb=" C VAL A 172 " pdb=" N PRO A 173 " ideal model delta sigma weight residual 1.331 1.362 -0.031 1.20e-02 6.94e+03 6.47e+00 bond pdb=" N ASN A 175 " pdb=" CA ASN A 175 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.66e+00 ... (remaining 2232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 2898 1.54 - 3.09: 133 3.09 - 4.63: 21 4.63 - 6.18: 3 6.18 - 7.72: 3 Bond angle restraints: 3058 Sorted by residual: angle pdb=" N MET A 174 " pdb=" CA MET A 174 " pdb=" C MET A 174 " ideal model delta sigma weight residual 111.28 107.82 3.46 1.09e+00 8.42e-01 1.01e+01 angle pdb=" N VAL A 55 " pdb=" CA VAL A 55 " pdb=" C VAL A 55 " ideal model delta sigma weight residual 110.62 107.13 3.49 1.14e+00 7.69e-01 9.39e+00 angle pdb=" N ASN A 380 " pdb=" CA ASN A 380 " pdb=" C ASN A 380 " ideal model delta sigma weight residual 109.81 116.26 -6.45 2.21e+00 2.05e-01 8.51e+00 angle pdb=" CA ASN A 175 " pdb=" C ASN A 175 " pdb=" O ASN A 175 " ideal model delta sigma weight residual 120.55 117.51 3.04 1.06e+00 8.90e-01 8.22e+00 angle pdb=" CA ASN A 380 " pdb=" C ASN A 380 " pdb=" N PRO A 381 " ideal model delta sigma weight residual 118.44 122.88 -4.44 1.59e+00 3.96e-01 7.79e+00 ... (remaining 3053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 1219 16.98 - 33.95: 96 33.95 - 50.92: 19 50.92 - 67.90: 10 67.90 - 84.87: 3 Dihedral angle restraints: 1347 sinusoidal: 547 harmonic: 800 Sorted by residual: dihedral pdb=" CB CYS A 77 " pdb=" SG CYS A 77 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual 93.00 176.45 -83.45 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CB CYS A 74 " pdb=" SG CYS A 74 " pdb=" SG CYS A 146 " pdb=" CB CYS A 146 " ideal model delta sinusoidal sigma weight residual 93.00 160.12 -67.12 1 1.00e+01 1.00e-02 5.87e+01 dihedral pdb=" CA VAL A 378 " pdb=" C VAL A 378 " pdb=" N VAL A 379 " pdb=" CA VAL A 379 " ideal model delta harmonic sigma weight residual -180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 1344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 309 0.058 - 0.116: 57 0.116 - 0.174: 7 0.174 - 0.232: 2 0.232 - 0.290: 1 Chirality restraints: 376 Sorted by residual: chirality pdb=" CA ASN A 380 " pdb=" N ASN A 380 " pdb=" C ASN A 380 " pdb=" CB ASN A 380 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA VAL A 55 " pdb=" N VAL A 55 " pdb=" C VAL A 55 " pdb=" CB VAL A 55 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CA MET A 177 " pdb=" N MET A 177 " pdb=" C MET A 177 " pdb=" CB MET A 177 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.83e-01 ... (remaining 373 not shown) Planarity restraints: 357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 343 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO A 344 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 179 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C TYR A 179 " -0.031 2.00e-02 2.50e+03 pdb=" O TYR A 179 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE A 180 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 174 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" C MET A 174 " -0.028 2.00e-02 2.50e+03 pdb=" O MET A 174 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN A 175 " 0.010 2.00e-02 2.50e+03 ... (remaining 354 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 483 2.79 - 3.32: 2309 3.32 - 3.84: 3704 3.84 - 4.37: 4215 4.37 - 4.90: 7260 Nonbonded interactions: 17971 Sorted by model distance: nonbonded pdb=" O VAL A 371 " pdb=" OG1 THR A 375 " model vdw 2.262 3.040 nonbonded pdb=" O LEU A 37 " pdb=" ND2 ASN A 42 " model vdw 2.337 3.120 nonbonded pdb=" OD1 ASN A 144 " pdb=" N CYS A 146 " model vdw 2.410 3.120 nonbonded pdb=" OD1 ASN A 349 " pdb=" N15 ZMA A 502 " model vdw 2.450 3.120 nonbonded pdb=" OG1 THR A 41 " pdb=" OD2 ASP A 101 " model vdw 2.454 3.040 ... (remaining 17966 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=0.40 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: 1.000 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: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.850 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 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 0.036 2239 Z= 0.315 Angle : 0.730 7.720 3062 Z= 0.433 Chirality : 0.048 0.290 376 Planarity : 0.005 0.062 357 Dihedral : 13.446 84.873 821 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.91 % Allowed : 1.36 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.51), residues: 268 helix: 1.71 (0.34), residues: 222 sheet: None (None), residues: 0 loop : 0.00 (0.91), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 111 TYR 0.008 0.001 TYR A 176 PHE 0.010 0.001 PHE A 83 TRP 0.009 0.001 TRP A 342 HIS 0.001 0.000 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 2237) covalent geometry : angle 0.72904 ( 3058) SS BOND : bond 0.00147 ( 2) SS BOND : angle 1.02567 ( 4) hydrogen bonds : bond 0.15804 ( 171) hydrogen bonds : angle 5.46452 ( 513) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.043 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 14 average time/residue: 0.0199 time to fit residues: 0.4290 Evaluate side-chains 11 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 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 = 0.4367 r_free = 0.4367 target = 0.212533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.172036 restraints weight = 4699.492| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.47 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3969 r_free = 0.3969 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3969 r_free = 0.3969 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2239 Z= 0.150 Angle : 0.595 7.595 3062 Z= 0.309 Chirality : 0.043 0.268 376 Planarity : 0.005 0.061 357 Dihedral : 10.542 84.951 393 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.50), residues: 268 helix: 1.98 (0.33), residues: 233 sheet: None (None), residues: 0 loop : 0.14 (1.01), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 205 TYR 0.008 0.001 TYR A 43 PHE 0.011 0.001 PHE A 83 TRP 0.008 0.001 TRP A 342 HIS 0.008 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 2237) covalent geometry : angle 0.59472 ( 3058) SS BOND : bond 0.00258 ( 2) SS BOND : angle 1.00079 ( 4) hydrogen bonds : bond 0.04316 ( 171) hydrogen bonds : angle 3.87359 ( 513) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.044 Fit side-chains REVERT: A 183 PHE cc_start: 0.7793 (m-80) cc_final: 0.7352 (m-80) outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0468 time to fit residues: 0.6506 Evaluate side-chains 11 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 17 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4348 r_free = 0.4348 target = 0.209765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.167139 restraints weight = 6482.984| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 5.41 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3863 r_free = 0.3863 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3863 r_free = 0.3863 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2239 Z= 0.140 Angle : 0.568 7.130 3062 Z= 0.290 Chirality : 0.041 0.239 376 Planarity : 0.005 0.061 357 Dihedral : 10.514 87.928 393 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.45 % Allowed : 5.91 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.50), residues: 268 helix: 2.19 (0.34), residues: 228 sheet: None (None), residues: 0 loop : -0.56 (0.88), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 102 TYR 0.021 0.001 TYR A 176 PHE 0.010 0.001 PHE A 83 TRP 0.005 0.001 TRP A 342 HIS 0.005 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 2237) covalent geometry : angle 0.56742 ( 3058) SS BOND : bond 0.00246 ( 2) SS BOND : angle 0.90604 ( 4) hydrogen bonds : bond 0.03973 ( 171) hydrogen bonds : angle 3.72494 ( 513) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.043 Fit side-chains REVERT: A 183 PHE cc_start: 0.7828 (m-80) cc_final: 0.7279 (m-80) outliers start: 1 outliers final: 0 residues processed: 13 average time/residue: 0.0389 time to fit residues: 0.6474 Evaluate side-chains 11 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4463 r_free = 0.4463 target = 0.219375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.187546 restraints weight = 5989.799| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 3.04 r_work: 0.3229 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2239 Z= 0.132 Angle : 0.554 6.613 3062 Z= 0.281 Chirality : 0.040 0.219 376 Planarity : 0.005 0.059 357 Dihedral : 10.568 89.647 393 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.45 % Allowed : 7.73 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.50), residues: 268 helix: 2.24 (0.34), residues: 228 sheet: None (None), residues: 0 loop : -0.66 (0.88), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 102 TYR 0.023 0.001 TYR A 176 PHE 0.008 0.001 PHE A 201 TRP 0.006 0.001 TRP A 342 HIS 0.005 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 2237) covalent geometry : angle 0.55348 ( 3058) SS BOND : bond 0.00264 ( 2) SS BOND : angle 0.81554 ( 4) hydrogen bonds : bond 0.03793 ( 171) hydrogen bonds : angle 3.69422 ( 513) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.044 Fit side-chains REVERT: A 183 PHE cc_start: 0.8044 (m-80) cc_final: 0.7506 (m-80) outliers start: 1 outliers final: 0 residues processed: 12 average time/residue: 0.0486 time to fit residues: 0.7282 Evaluate side-chains 10 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 25 optimal weight: 0.0270 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 10 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 = 0.4366 r_free = 0.4366 target = 0.211454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.174778 restraints weight = 4866.267| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 2.46 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4011 r_free = 0.4011 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4011 r_free = 0.4011 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 2239 Z= 0.119 Angle : 0.524 7.984 3062 Z= 0.262 Chirality : 0.039 0.155 376 Planarity : 0.005 0.057 357 Dihedral : 10.407 88.964 393 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.91 % Allowed : 8.18 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.50), residues: 268 helix: 2.35 (0.34), residues: 228 sheet: None (None), residues: 0 loop : -0.83 (0.84), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 102 TYR 0.023 0.001 TYR A 176 PHE 0.008 0.001 PHE A 201 TRP 0.004 0.001 TRP A 342 HIS 0.005 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 2237) covalent geometry : angle 0.52335 ( 3058) SS BOND : bond 0.00268 ( 2) SS BOND : angle 0.78879 ( 4) hydrogen bonds : bond 0.03575 ( 171) hydrogen bonds : angle 3.54713 ( 513) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.045 Fit side-chains REVERT: A 183 PHE cc_start: 0.7651 (m-80) cc_final: 0.7274 (m-80) outliers start: 2 outliers final: 1 residues processed: 12 average time/residue: 0.0426 time to fit residues: 0.6525 Evaluate side-chains 12 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.2980 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.204268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.163464 restraints weight = 7841.861| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 7.41 r_work: 0.3425 rms_B_bonded: 6.65 restraints_weight: 2.0000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 2239 Z= 0.157 Angle : 0.591 7.862 3062 Z= 0.292 Chirality : 0.041 0.176 376 Planarity : 0.005 0.056 357 Dihedral : 10.717 86.305 393 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.45 % Allowed : 8.64 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.50), residues: 268 helix: 2.17 (0.34), residues: 228 sheet: None (None), residues: 0 loop : -0.89 (0.82), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 392 TYR 0.021 0.001 TYR A 176 PHE 0.009 0.001 PHE A 201 TRP 0.005 0.001 TRP A 342 HIS 0.006 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 2237) covalent geometry : angle 0.59120 ( 3058) SS BOND : bond 0.00272 ( 2) SS BOND : angle 0.78727 ( 4) hydrogen bonds : bond 0.03994 ( 171) hydrogen bonds : angle 3.59872 ( 513) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.044 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 13 average time/residue: 0.0406 time to fit residues: 0.7001 Evaluate side-chains 12 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 1 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.4324 r_free = 0.4324 target = 0.206561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.166793 restraints weight = 6554.943| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 6.59 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3899 r_free = 0.3899 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3899 r_free = 0.3899 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2239 Z= 0.130 Angle : 0.565 10.048 3062 Z= 0.276 Chirality : 0.040 0.165 376 Planarity : 0.005 0.056 357 Dihedral : 10.508 87.626 393 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.91 % Allowed : 9.55 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.74 (0.50), residues: 268 helix: 2.26 (0.34), residues: 228 sheet: None (None), residues: 0 loop : -0.86 (0.81), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 205 TYR 0.020 0.001 TYR A 176 PHE 0.009 0.001 PHE A 201 TRP 0.004 0.001 TRP A 32 HIS 0.005 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 2237) covalent geometry : angle 0.56476 ( 3058) SS BOND : bond 0.00263 ( 2) SS BOND : angle 0.74362 ( 4) hydrogen bonds : bond 0.03721 ( 171) hydrogen bonds : angle 3.57129 ( 513) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 12 time to evaluate : 0.067 Fit side-chains REVERT: A 177 MET cc_start: 0.6824 (mmm) cc_final: 0.6581 (mmt) outliers start: 2 outliers final: 1 residues processed: 14 average time/residue: 0.0585 time to fit residues: 1.0433 Evaluate side-chains 12 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.216089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.178118 restraints weight = 6663.801| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 7.29 r_work: 0.3155 rms_B_bonded: 5.84 restraints_weight: 2.0000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2239 Z= 0.143 Angle : 0.574 9.374 3062 Z= 0.281 Chirality : 0.040 0.169 376 Planarity : 0.005 0.056 357 Dihedral : 10.570 88.374 393 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.91 % Allowed : 10.45 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.51), residues: 268 helix: 2.19 (0.34), residues: 228 sheet: None (None), residues: 0 loop : -0.47 (0.91), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 102 TYR 0.020 0.001 TYR A 176 PHE 0.009 0.001 PHE A 201 TRP 0.004 0.001 TRP A 32 HIS 0.005 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 2237) covalent geometry : angle 0.57417 ( 3058) SS BOND : bond 0.00241 ( 2) SS BOND : angle 0.77717 ( 4) hydrogen bonds : bond 0.03855 ( 171) hydrogen bonds : angle 3.58282 ( 513) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.072 Fit side-chains REVERT: A 376 ASN cc_start: 0.7933 (OUTLIER) cc_final: 0.7727 (t0) outliers start: 2 outliers final: 1 residues processed: 12 average time/residue: 0.0689 time to fit residues: 1.0542 Evaluate side-chains 13 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 376 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.210498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.181467 restraints weight = 6451.084| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 4.31 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2239 Z= 0.130 Angle : 0.563 9.484 3062 Z= 0.275 Chirality : 0.039 0.163 376 Planarity : 0.005 0.056 357 Dihedral : 10.522 88.737 393 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.91 % Allowed : 11.36 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.79 (0.51), residues: 268 helix: 2.22 (0.34), residues: 228 sheet: None (None), residues: 0 loop : -0.34 (0.92), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 205 TYR 0.020 0.001 TYR A 176 PHE 0.009 0.001 PHE A 201 TRP 0.004 0.001 TRP A 32 HIS 0.005 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 2237) covalent geometry : angle 0.56305 ( 3058) SS BOND : bond 0.00240 ( 2) SS BOND : angle 0.75156 ( 4) hydrogen bonds : bond 0.03740 ( 171) hydrogen bonds : angle 3.55720 ( 513) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.067 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 12 average time/residue: 0.0637 time to fit residues: 0.9726 Evaluate side-chains 11 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 0.0000 chunk 18 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 7 optimal weight: 0.0370 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.3862 ------------------------------------------------------------------------------- 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 = 0.4393 r_free = 0.4393 target = 0.212665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.185398 restraints weight = 6128.857| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.91 r_work: 0.3317 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2239 Z= 0.112 Angle : 0.533 9.721 3062 Z= 0.260 Chirality : 0.038 0.152 376 Planarity : 0.005 0.056 357 Dihedral : 10.187 88.708 393 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.45 % Allowed : 11.36 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.96 (0.51), residues: 268 helix: 2.35 (0.34), residues: 228 sheet: None (None), residues: 0 loop : -0.37 (0.87), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 205 TYR 0.018 0.001 TYR A 176 PHE 0.008 0.001 PHE A 201 TRP 0.004 0.001 TRP A 32 HIS 0.004 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 2237) covalent geometry : angle 0.53304 ( 3058) SS BOND : bond 0.00221 ( 2) SS BOND : angle 0.69606 ( 4) hydrogen bonds : bond 0.03439 ( 171) hydrogen bonds : angle 3.53149 ( 513) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.044 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 11 average time/residue: 0.0450 time to fit residues: 0.6300 Evaluate side-chains 11 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 3 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4469 r_free = 0.4469 target = 0.222411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.185229 restraints weight = 6616.623| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 4.68 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3501 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2239 Z= 0.133 Angle : 0.559 8.620 3062 Z= 0.274 Chirality : 0.040 0.162 376 Planarity : 0.005 0.055 357 Dihedral : 10.296 88.159 393 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.91 % Allowed : 10.45 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.50), residues: 268 helix: 2.26 (0.34), residues: 228 sheet: None (None), residues: 0 loop : -0.39 (0.87), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 205 TYR 0.016 0.001 TYR A 176 PHE 0.009 0.001 PHE A 201 TRP 0.004 0.001 TRP A 342 HIS 0.005 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 2237) covalent geometry : angle 0.55831 ( 3058) SS BOND : bond 0.00230 ( 2) SS BOND : angle 0.74943 ( 4) hydrogen bonds : bond 0.03685 ( 171) hydrogen bonds : angle 3.55921 ( 513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 510.61 seconds wall clock time: 9 minutes 22.55 seconds (562.55 seconds total)