Starting phenix.real_space_refine on Wed Mar 4 00:30:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nkd_12438/03_2026/7nkd_12438.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nkd_12438/03_2026/7nkd_12438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nkd_12438/03_2026/7nkd_12438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nkd_12438/03_2026/7nkd_12438.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nkd_12438/03_2026/7nkd_12438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nkd_12438/03_2026/7nkd_12438.map" } resolution = 3.12 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= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 5 5.16 5 C 2952 2.51 5 N 852 2.21 5 O 978 1.98 5 H 4768 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9555 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1346 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain breaks: 6 Chain: "B" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 652 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain breaks: 4 Chain: "C" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 448 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain breaks: 2 Chain: "D" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 601 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 2, 'TRANS': 36} Chain breaks: 3 Chain: "E" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 620 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain breaks: 3 Chain: "F" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 277 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain breaks: 3 Chain: "d" Number of atoms: 5084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5084 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 10, 'TRANS': 325} Chain: "b" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 527 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Time building chain proxies: 2.09, per 1000 atoms: 0.22 Number of scatterers: 9555 At special positions: 0 Unit cell: (111.22, 73.04, 83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 5 16.00 O 978 8.00 N 852 7.00 C 2952 6.00 H 4768 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 232.1 milliseconds 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1182 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 5 sheets defined 51.6% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 7 through 21 removed outlier: 3.529A pdb=" N ILE A 15 " --> pdb=" O ILE A 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.593A pdb=" N ALA B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP B 17 " --> pdb=" O GLY B 13 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE B 22 " --> pdb=" O TYR B 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'd' and resid 110 through 138 Processing helix chain 'd' and resid 139 through 157 removed outlier: 3.559A pdb=" N GLN d 156 " --> pdb=" O SER d 152 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 192 removed outlier: 3.729A pdb=" N GLY d 192 " --> pdb=" O ASP d 188 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 216 Processing helix chain 'd' and resid 216 through 225 Processing helix chain 'd' and resid 230 through 242 Processing helix chain 'd' and resid 246 through 259 removed outlier: 3.577A pdb=" N ASN d 259 " --> pdb=" O THR d 255 " (cutoff:3.500A) Processing helix chain 'd' and resid 263 through 286 removed outlier: 3.882A pdb=" N LEU d 267 " --> pdb=" O THR d 263 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE d 268 " --> pdb=" O GLU d 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 288 through 306 Processing helix chain 'd' and resid 306 through 314 Processing helix chain 'd' and resid 319 through 331 Processing helix chain 'd' and resid 338 through 351 Processing helix chain 'd' and resid 356 through 372 removed outlier: 3.742A pdb=" N ARG d 372 " --> pdb=" O ALA d 368 " (cutoff:3.500A) Processing helix chain 'd' and resid 386 through 402 Processing helix chain 'd' and resid 412 through 416 Processing helix chain 'd' and resid 431 through 442 Processing helix chain 'b' and resid 131 through 145 Processing helix chain 'b' and resid 147 through 161 removed outlier: 3.557A pdb=" N LEU b 151 " --> pdb=" O SER b 147 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 46 removed outlier: 5.782A pdb=" N GLU A 30 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A 93 " --> pdb=" O GLU A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 46 removed outlier: 5.926A pdb=" N VAL d 375 " --> pdb=" O SER d 406 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN d 408 " --> pdb=" O VAL d 375 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA d 377 " --> pdb=" O GLN d 408 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 33 through 36 removed outlier: 6.476A pdb=" N HIS B 43 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 11 through 14 removed outlier: 6.466A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY D 58 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG D 63 " --> pdb=" O HIS D 56 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N HIS D 56 " --> pdb=" O ARG D 63 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 56 through 58 removed outlier: 6.268A pdb=" N HIS E 56 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG E 63 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASP E 21 " --> pdb=" O VAL E 13 " (cutoff:3.500A) 279 hydrogen bonds defined for protein. 804 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: 2.20 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4766 1.03 - 1.23: 2 1.23 - 1.42: 1901 1.42 - 1.61: 2901 1.61 - 1.81: 8 Bond restraints: 9578 Sorted by residual: bond pdb=" N THR d 166 " pdb=" CA THR d 166 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.94e+00 bond pdb=" N ILE d 164 " pdb=" CA ILE d 164 " ideal model delta sigma weight residual 1.474 1.458 0.017 1.57e-02 4.06e+03 1.13e+00 bond pdb=" CA ILE d 164 " pdb=" CB ILE d 164 " ideal model delta sigma weight residual 1.532 1.544 -0.012 1.42e-02 4.96e+03 6.61e-01 bond pdb=" C LEU d 416 " pdb=" N GLY d 417 " ideal model delta sigma weight residual 1.321 1.330 -0.009 1.24e-02 6.50e+03 5.46e-01 bond pdb=" C ASP d 412 " pdb=" O ASP d 412 " ideal model delta sigma weight residual 1.238 1.247 -0.009 1.28e-02 6.10e+03 5.13e-01 ... (remaining 9573 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 16447 1.05 - 2.11: 831 2.11 - 3.16: 24 3.16 - 4.22: 16 4.22 - 5.27: 1 Bond angle restraints: 17319 Sorted by residual: angle pdb=" N ILE d 164 " pdb=" CA ILE d 164 " pdb=" C ILE d 164 " ideal model delta sigma weight residual 106.21 109.21 -3.00 1.07e+00 8.73e-01 7.87e+00 angle pdb=" C THR d 166 " pdb=" CA THR d 166 " pdb=" CB THR d 166 " ideal model delta sigma weight residual 110.42 115.69 -5.27 1.99e+00 2.53e-01 7.01e+00 angle pdb=" C SER C 21 " pdb=" N PHE C 22 " pdb=" CA PHE C 22 " ideal model delta sigma weight residual 122.56 118.63 3.93 1.72e+00 3.38e-01 5.21e+00 angle pdb=" CA GLY d 417 " pdb=" C GLY d 417 " pdb=" N GLY d 418 " ideal model delta sigma weight residual 115.34 116.84 -1.50 8.40e-01 1.42e+00 3.17e+00 angle pdb=" C ASP d 165 " pdb=" N THR d 166 " pdb=" CA THR d 166 " ideal model delta sigma weight residual 121.54 124.61 -3.07 1.91e+00 2.74e-01 2.58e+00 ... (remaining 17314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 3993 17.50 - 34.99: 301 34.99 - 52.49: 95 52.49 - 69.99: 22 69.99 - 87.48: 10 Dihedral angle restraints: 4421 sinusoidal: 2498 harmonic: 1923 Sorted by residual: dihedral pdb=" CB GLU C 12 " pdb=" CG GLU C 12 " pdb=" CD GLU C 12 " pdb=" OE1 GLU C 12 " ideal model delta sinusoidal sigma weight residual 0.00 -87.48 87.48 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA ASP D 59 " pdb=" CB ASP D 59 " pdb=" CG ASP D 59 " pdb=" OD1 ASP D 59 " ideal model delta sinusoidal sigma weight residual -30.00 -84.12 54.12 1 2.00e+01 2.50e-03 9.93e+00 dihedral pdb=" CG ARG D 26 " pdb=" CD ARG D 26 " pdb=" NE ARG D 26 " pdb=" CZ ARG D 26 " ideal model delta sinusoidal sigma weight residual 180.00 138.41 41.59 2 1.50e+01 4.44e-03 9.40e+00 ... (remaining 4418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 535 0.026 - 0.053: 158 0.053 - 0.079: 53 0.079 - 0.105: 38 0.105 - 0.132: 18 Chirality restraints: 802 Sorted by residual: chirality pdb=" CA ILE A 85 " pdb=" N ILE A 85 " pdb=" C ILE A 85 " pdb=" CB ILE A 85 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA VAL D 29 " pdb=" N VAL D 29 " pdb=" C VAL D 29 " pdb=" CB VAL D 29 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA ILE d 428 " pdb=" N ILE d 428 " pdb=" C ILE d 428 " pdb=" CB ILE d 428 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 799 not shown) Planarity restraints: 1441 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 29 " -0.006 2.00e-02 2.50e+03 1.18e-02 1.39e+00 pdb=" CD GLU A 29 " 0.020 2.00e-02 2.50e+03 pdb=" OE1 GLU A 29 " -0.007 2.00e-02 2.50e+03 pdb=" OE2 GLU A 29 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN b 136 " -0.005 2.00e-02 2.50e+03 9.30e-03 1.30e+00 pdb=" CD GLN b 136 " 0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN b 136 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 GLN b 136 " -0.009 2.00e-02 2.50e+03 pdb="HE21 GLN b 136 " 0.001 2.00e-02 2.50e+03 pdb="HE22 GLN b 136 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER b 152 " -0.005 2.00e-02 2.50e+03 1.06e-02 1.11e+00 pdb=" C SER b 152 " 0.018 2.00e-02 2.50e+03 pdb=" O SER b 152 " -0.007 2.00e-02 2.50e+03 pdb=" N ALA b 153 " -0.006 2.00e-02 2.50e+03 ... (remaining 1438 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 651 2.20 - 2.80: 20245 2.80 - 3.40: 26639 3.40 - 4.00: 33554 4.00 - 4.60: 51795 Nonbonded interactions: 132884 Sorted by model distance: nonbonded pdb=" OE1 GLU B 71 " pdb=" H GLU B 71 " model vdw 1.596 2.450 nonbonded pdb=" OE1 GLU A 71 " pdb=" H GLU A 71 " model vdw 1.611 2.450 nonbonded pdb=" HG1 THR d 263 " pdb=" OD1 ASN d 266 " model vdw 1.616 2.450 nonbonded pdb=" HG SER d 179 " pdb=" O ARG d 260 " model vdw 1.638 2.450 nonbonded pdb=" O ARG F 11 " pdb=" H GLU F 23 " model vdw 1.647 2.450 ... (remaining 132879 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name HG \ 22 or name HG23)) or resid 9 through 30 or resid 55 through 81)) selection = (chain 'E' and (resid 8 through 15 or (resid 20 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 \ or name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 21 \ through 30 or (resid 55 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 o \ r name HG2 or name HG3 or name HE21 or name HE22)) or resid 56 through 81)) } 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: 10.910 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: 0.060 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.710 Find NCS groups from input model: 0.030 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.003 0.024 4810 Z= 0.131 Angle : 0.452 5.270 6490 Z= 0.252 Chirality : 0.037 0.132 802 Planarity : 0.003 0.032 848 Dihedral : 14.504 87.484 1754 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: 2.45 (0.37), residues: 585 helix: 2.72 (0.30), residues: 314 sheet: -1.17 (0.70), residues: 57 loop : 0.90 (0.47), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 26 TYR 0.006 0.001 TYR A 18 PHE 0.009 0.001 PHE d 187 TRP 0.003 0.001 TRP d 261 HIS 0.001 0.000 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 4810) covalent geometry : angle 0.45171 ( 6490) hydrogen bonds : bond 0.13898 ( 277) hydrogen bonds : angle 6.00059 ( 804) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1072 time to fit residues: 9.1575 Evaluate side-chains 49 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 0.1980 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.0770 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.0980 chunk 25 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 overall best weight: 0.2938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.074049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.058466 restraints weight = 41251.243| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.38 r_work: 0.2993 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4810 Z= 0.124 Angle : 0.482 8.769 6490 Z= 0.256 Chirality : 0.039 0.142 802 Planarity : 0.003 0.030 848 Dihedral : 3.427 12.603 665 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.58 % Allowed : 3.86 % Favored : 95.56 % 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: 2.59 (0.36), residues: 585 helix: 3.03 (0.29), residues: 317 sheet: -1.03 (0.67), residues: 57 loop : 0.53 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 75 TYR 0.006 0.001 TYR B 18 PHE 0.013 0.001 PHE C 22 TRP 0.004 0.001 TRP d 261 HIS 0.001 0.000 HIS d 222 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 4810) covalent geometry : angle 0.48241 ( 6490) hydrogen bonds : bond 0.04157 ( 277) hydrogen bonds : angle 4.49338 ( 804) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8405 (tp30) cc_final: 0.8135 (tp30) outliers start: 3 outliers final: 2 residues processed: 51 average time/residue: 0.0832 time to fit residues: 6.5663 Evaluate side-chains 48 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain F residue 61 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 0.0870 chunk 25 optimal weight: 0.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.073229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.058075 restraints weight = 41795.703| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.30 r_work: 0.2969 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4810 Z= 0.205 Angle : 0.487 6.385 6490 Z= 0.262 Chirality : 0.039 0.137 802 Planarity : 0.003 0.033 848 Dihedral : 3.481 13.665 665 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.39 % Allowed : 5.02 % Favored : 94.59 % 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: 2.49 (0.35), residues: 585 helix: 3.03 (0.28), residues: 317 sheet: -1.10 (0.64), residues: 57 loop : 0.35 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 26 TYR 0.007 0.001 TYR B 18 PHE 0.014 0.001 PHE C 22 TRP 0.005 0.002 TRP d 261 HIS 0.003 0.001 HIS d 410 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 4810) covalent geometry : angle 0.48710 ( 6490) hydrogen bonds : bond 0.03762 ( 277) hydrogen bonds : angle 4.37971 ( 804) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8408 (tp30) cc_final: 0.8120 (tp30) outliers start: 2 outliers final: 2 residues processed: 45 average time/residue: 0.0799 time to fit residues: 5.8137 Evaluate side-chains 46 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain F residue 61 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 47 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 2 optimal weight: 0.0870 chunk 44 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.073251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.058068 restraints weight = 41974.873| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.29 r_work: 0.2966 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4810 Z= 0.166 Angle : 0.465 6.288 6490 Z= 0.247 Chirality : 0.039 0.134 802 Planarity : 0.003 0.035 848 Dihedral : 3.442 13.037 665 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.39 % Allowed : 6.37 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.59 (0.36), residues: 585 helix: 3.13 (0.29), residues: 317 sheet: -1.04 (0.64), residues: 57 loop : 0.36 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG d 115 TYR 0.008 0.001 TYR B 18 PHE 0.014 0.001 PHE C 22 TRP 0.005 0.001 TRP d 261 HIS 0.002 0.001 HIS d 410 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 4810) covalent geometry : angle 0.46511 ( 6490) hydrogen bonds : bond 0.03432 ( 277) hydrogen bonds : angle 4.17420 ( 804) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8427 (tp30) cc_final: 0.8132 (tp30) outliers start: 2 outliers final: 2 residues processed: 46 average time/residue: 0.0811 time to fit residues: 6.0559 Evaluate side-chains 47 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain F residue 61 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 0.0980 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 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 = 0.3465 r_free = 0.3465 target = 0.073090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.057953 restraints weight = 41637.904| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.28 r_work: 0.2969 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4810 Z= 0.159 Angle : 0.457 5.802 6490 Z= 0.243 Chirality : 0.039 0.135 802 Planarity : 0.003 0.036 848 Dihedral : 3.406 13.223 665 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.39 % Allowed : 6.56 % Favored : 93.05 % 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: 2.66 (0.36), residues: 585 helix: 3.17 (0.28), residues: 317 sheet: -0.97 (0.64), residues: 57 loop : 0.41 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG d 115 TYR 0.008 0.001 TYR B 18 PHE 0.014 0.001 PHE C 22 TRP 0.005 0.001 TRP d 261 HIS 0.002 0.001 HIS d 378 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 4810) covalent geometry : angle 0.45714 ( 6490) hydrogen bonds : bond 0.03347 ( 277) hydrogen bonds : angle 4.10496 ( 804) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8431 (tp30) cc_final: 0.8130 (tp30) outliers start: 2 outliers final: 2 residues processed: 45 average time/residue: 0.0764 time to fit residues: 5.5760 Evaluate side-chains 47 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain F residue 61 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.072484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.056907 restraints weight = 41840.283| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.37 r_work: 0.2948 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4810 Z= 0.215 Angle : 0.481 5.115 6490 Z= 0.258 Chirality : 0.039 0.136 802 Planarity : 0.003 0.036 848 Dihedral : 3.493 13.550 665 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.39 % Allowed : 7.72 % Favored : 91.89 % 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: 2.55 (0.35), residues: 585 helix: 3.10 (0.28), residues: 317 sheet: -0.96 (0.64), residues: 57 loop : 0.29 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG d 115 TYR 0.009 0.001 TYR B 18 PHE 0.014 0.001 PHE C 22 TRP 0.006 0.002 TRP d 261 HIS 0.002 0.001 HIS d 378 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 4810) covalent geometry : angle 0.48052 ( 6490) hydrogen bonds : bond 0.03355 ( 277) hydrogen bonds : angle 4.15132 ( 804) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8622 (p0) cc_final: 0.8366 (p0) REVERT: A 43 HIS cc_start: 0.8575 (m90) cc_final: 0.8260 (m90) REVERT: F 23 GLU cc_start: 0.8416 (tp30) cc_final: 0.8097 (tp30) outliers start: 2 outliers final: 1 residues processed: 45 average time/residue: 0.0815 time to fit residues: 5.8987 Evaluate side-chains 46 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 52 optimal weight: 0.3980 chunk 42 optimal weight: 0.1980 chunk 11 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 47 optimal weight: 0.2980 chunk 19 optimal weight: 0.0470 chunk 9 optimal weight: 1.9990 overall best weight: 0.2878 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.073501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.057934 restraints weight = 41471.119| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.35 r_work: 0.2975 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4810 Z= 0.104 Angle : 0.444 8.210 6490 Z= 0.231 Chirality : 0.039 0.139 802 Planarity : 0.003 0.036 848 Dihedral : 3.332 12.605 665 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.19 % Allowed : 8.69 % Favored : 91.12 % 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: 2.90 (0.36), residues: 585 helix: 3.36 (0.29), residues: 317 sheet: -0.81 (0.65), residues: 57 loop : 0.52 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG d 115 TYR 0.005 0.001 TYR A 18 PHE 0.014 0.001 PHE C 22 TRP 0.003 0.001 TRP d 261 HIS 0.001 0.000 HIS d 222 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 4810) covalent geometry : angle 0.44380 ( 6490) hydrogen bonds : bond 0.03089 ( 277) hydrogen bonds : angle 3.91458 ( 804) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8416 (tp30) cc_final: 0.8132 (tp30) outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 0.0838 time to fit residues: 6.3774 Evaluate side-chains 46 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 0.0980 chunk 46 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.072798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.057219 restraints weight = 41886.445| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.34 r_work: 0.2960 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4810 Z= 0.191 Angle : 0.470 7.373 6490 Z= 0.249 Chirality : 0.039 0.135 802 Planarity : 0.003 0.036 848 Dihedral : 3.383 13.283 665 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % 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 (0.36), residues: 585 helix: 3.27 (0.29), residues: 317 sheet: -0.76 (0.65), residues: 57 loop : 0.42 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 26 TYR 0.007 0.001 TYR B 18 PHE 0.010 0.001 PHE d 187 TRP 0.005 0.002 TRP d 261 HIS 0.002 0.001 HIS d 378 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 4810) covalent geometry : angle 0.46962 ( 6490) hydrogen bonds : bond 0.03169 ( 277) hydrogen bonds : angle 4.02061 ( 804) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8630 (p0) cc_final: 0.8397 (p0) REVERT: A 43 HIS cc_start: 0.8554 (m90) cc_final: 0.8292 (m90) REVERT: F 23 GLU cc_start: 0.8406 (tp30) cc_final: 0.8110 (tp30) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0836 time to fit residues: 6.3203 Evaluate side-chains 45 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 51 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 0.0980 chunk 48 optimal weight: 0.0980 chunk 38 optimal weight: 0.3980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.073411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.057765 restraints weight = 41372.929| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.39 r_work: 0.2972 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4810 Z= 0.114 Angle : 0.444 8.582 6490 Z= 0.230 Chirality : 0.039 0.136 802 Planarity : 0.003 0.036 848 Dihedral : 3.289 12.510 665 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % 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: 3.02 (0.36), residues: 585 helix: 3.44 (0.29), residues: 317 sheet: -0.65 (0.66), residues: 57 loop : 0.56 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 26 TYR 0.005 0.001 TYR A 18 PHE 0.008 0.001 PHE d 187 TRP 0.003 0.001 TRP d 261 HIS 0.001 0.000 HIS d 222 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 4810) covalent geometry : angle 0.44437 ( 6490) hydrogen bonds : bond 0.03003 ( 277) hydrogen bonds : angle 3.84271 ( 804) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8631 (p0) cc_final: 0.8394 (p0) REVERT: A 43 HIS cc_start: 0.8558 (m90) cc_final: 0.8319 (m90) REVERT: F 23 GLU cc_start: 0.8404 (tp30) cc_final: 0.7749 (tp30) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0930 time to fit residues: 6.8313 Evaluate side-chains 47 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 39 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 0.0570 chunk 36 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 4 optimal weight: 0.0870 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 0.0570 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.0770 overall best weight: 0.1752 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.073890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.058308 restraints weight = 41138.178| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.38 r_work: 0.2983 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4810 Z= 0.089 Angle : 0.440 8.989 6490 Z= 0.226 Chirality : 0.038 0.138 802 Planarity : 0.003 0.036 848 Dihedral : 3.184 12.231 665 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % 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: 3.13 (0.36), residues: 585 helix: 3.51 (0.29), residues: 317 sheet: -0.56 (0.66), residues: 57 loop : 0.63 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 26 TYR 0.004 0.001 TYR A 18 PHE 0.008 0.001 PHE d 187 TRP 0.002 0.001 TRP d 261 HIS 0.001 0.000 HIS d 222 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 4810) covalent geometry : angle 0.44039 ( 6490) hydrogen bonds : bond 0.02890 ( 277) hydrogen bonds : angle 3.70885 ( 804) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8586 (p0) cc_final: 0.8323 (p0) REVERT: A 43 HIS cc_start: 0.8566 (m90) cc_final: 0.8335 (m90) REVERT: F 23 GLU cc_start: 0.8398 (tp30) cc_final: 0.7769 (tp30) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0762 time to fit residues: 5.9118 Evaluate side-chains 47 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 20 optimal weight: 0.5980 chunk 55 optimal weight: 0.0980 chunk 8 optimal weight: 0.2980 chunk 45 optimal weight: 0.8980 chunk 11 optimal weight: 0.1980 chunk 3 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 49 optimal weight: 0.1980 chunk 2 optimal weight: 0.2980 overall best weight: 0.2180 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.073711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.058212 restraints weight = 41615.846| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.37 r_work: 0.2984 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4810 Z= 0.094 Angle : 0.439 9.013 6490 Z= 0.225 Chirality : 0.038 0.137 802 Planarity : 0.003 0.036 848 Dihedral : 3.130 12.082 665 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.19 % Allowed : 9.27 % Favored : 90.54 % 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: 3.18 (0.36), residues: 585 helix: 3.54 (0.29), residues: 317 sheet: -0.51 (0.66), residues: 57 loop : 0.64 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 26 TYR 0.005 0.001 TYR A 18 PHE 0.008 0.001 PHE d 187 TRP 0.002 0.001 TRP d 261 HIS 0.001 0.000 HIS d 378 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 4810) covalent geometry : angle 0.43882 ( 6490) hydrogen bonds : bond 0.02843 ( 277) hydrogen bonds : angle 3.65849 ( 804) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2704.66 seconds wall clock time: 46 minutes 35.97 seconds (2795.97 seconds total)