Starting phenix.real_space_refine on Tue Feb 3 15:38:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9py7_72012/02_2026/9py7_72012.cif Found real_map, /net/cci-nas-00/data/ceres_data/9py7_72012/02_2026/9py7_72012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9py7_72012/02_2026/9py7_72012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9py7_72012/02_2026/9py7_72012.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9py7_72012/02_2026/9py7_72012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9py7_72012/02_2026/9py7_72012.map" } resolution = 2.8 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= 0.015 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 8 5.16 5 C 2759 2.51 5 N 749 2.21 5 O 832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s 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: 4348 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "L" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 855 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "A" Number of atoms: 2492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2492 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 27, 'TRANS': 279} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.17, per 1000 atoms: 0.27 Number of scatterers: 4348 At special positions: 0 Unit cell: (68.7872, 84.9092, 106.405, 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 8 16.00 O 832 8.00 N 749 7.00 C 2759 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 169 " 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1401 " - " ASN A 263 " " NAG B 1 " - " ASN A 641 " Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 178.5 milliseconds 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1010 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 8 sheets defined 23.5% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.746A pdb=" N GLN H 65 " --> pdb=" O PRO H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.739A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'A' and resid 110 through 132 removed outlier: 3.687A pdb=" N PHE A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Proline residue: A 118 - end of helix removed outlier: 4.094A pdb=" N ARG A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLN A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 181 through 188 Processing helix chain 'A' and resid 190 through 196 Processing helix chain 'A' and resid 208 through 215 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 222 through 227 removed outlier: 3.509A pdb=" N TYR A 226 " --> pdb=" O VAL A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 259 Processing helix chain 'A' and resid 623 through 628 Processing helix chain 'A' and resid 631 through 639 removed outlier: 3.521A pdb=" N TYR A 639 " --> pdb=" O THR A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 669 removed outlier: 3.971A pdb=" N ALA A 666 " --> pdb=" O ASN A 662 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.719A pdb=" N TYR H 99 " --> pdb=" O TYR H 33 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TYR H 33 " --> pdb=" O TYR H 99 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY H 44 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.160A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.963A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 55 through 60 Processing sheet with id=AA7, first strand: chain 'A' and resid 55 through 60 removed outlier: 3.507A pdb=" N SER A 101 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 149 through 150 165 hydrogen bonds defined for protein. 387 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: 0.66 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1408 1.34 - 1.46: 989 1.46 - 1.57: 2056 1.57 - 1.69: 0 1.69 - 1.81: 9 Bond restraints: 4462 Sorted by residual: bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.47e+00 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" CB VAL A 216 " pdb=" CG1 VAL A 216 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.14e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.14e+00 ... (remaining 4457 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 5783 1.06 - 2.12: 219 2.12 - 3.18: 56 3.18 - 4.25: 7 4.25 - 5.31: 10 Bond angle restraints: 6075 Sorted by residual: angle pdb=" CA TYR H 99 " pdb=" CB TYR H 99 " pdb=" CG TYR H 99 " ideal model delta sigma weight residual 113.90 118.74 -4.84 1.80e+00 3.09e-01 7.22e+00 angle pdb=" CA VAL A 146 " pdb=" C VAL A 146 " pdb=" N CYS A 147 " ideal model delta sigma weight residual 116.60 120.02 -3.42 1.45e+00 4.76e-01 5.55e+00 angle pdb=" N VAL A 146 " pdb=" CA VAL A 146 " pdb=" C VAL A 146 " ideal model delta sigma weight residual 109.34 113.67 -4.33 2.08e+00 2.31e-01 4.33e+00 angle pdb=" N VAL A 223 " pdb=" CA VAL A 223 " pdb=" C VAL A 223 " ideal model delta sigma weight residual 109.34 113.60 -4.26 2.08e+00 2.31e-01 4.19e+00 angle pdb=" CA TRP L 96 " pdb=" CB TRP L 96 " pdb=" CG TRP L 96 " ideal model delta sigma weight residual 113.60 117.45 -3.85 1.90e+00 2.77e-01 4.10e+00 ... (remaining 6070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.57: 2542 20.57 - 41.13: 124 41.13 - 61.70: 20 61.70 - 82.27: 5 82.27 - 102.83: 12 Dihedral angle restraints: 2703 sinusoidal: 1135 harmonic: 1568 Sorted by residual: dihedral pdb=" CB CYS A 147 " pdb=" SG CYS A 147 " pdb=" SG CYS A 169 " pdb=" CB CYS A 169 " ideal model delta sinusoidal sigma weight residual -86.00 -170.71 84.71 1 1.00e+01 1.00e-02 8.71e+01 dihedral pdb=" CA THR L 93 " pdb=" C THR L 93 " pdb=" N LEU L 94 " pdb=" CA LEU L 94 " ideal model delta harmonic sigma weight residual 180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" C1 NAG A1401 " pdb=" C2 NAG A1401 " pdb=" C3 NAG A1401 " pdb=" O3 NAG A1401 " ideal model delta sinusoidal sigma weight residual -175.09 -72.26 -102.83 1 3.00e+01 1.11e-03 1.30e+01 ... (remaining 2700 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 376 0.026 - 0.053: 179 0.053 - 0.079: 57 0.079 - 0.106: 39 0.106 - 0.132: 22 Chirality restraints: 673 Sorted by residual: chirality pdb=" CA ILE L 21 " pdb=" N ILE L 21 " pdb=" C ILE L 21 " pdb=" CB ILE L 21 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE A 655 " pdb=" N ILE A 655 " pdb=" C ILE A 655 " pdb=" CB ILE A 655 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" C1 NAG A1401 " pdb=" ND2 ASN A 263 " pdb=" C2 NAG A1401 " pdb=" O5 NAG A1401 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 670 not shown) Planarity restraints: 780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 173 " -0.023 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRO A 174 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 174 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 174 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 216 " -0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO A 217 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 217 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 217 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " -0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO L 59 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " -0.015 5.00e-02 4.00e+02 ... (remaining 777 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 871 2.78 - 3.31: 3911 3.31 - 3.84: 7004 3.84 - 4.37: 8249 4.37 - 4.90: 14575 Nonbonded interactions: 34610 Sorted by model distance: nonbonded pdb=" NZ LYS L 39 " pdb=" O GLU L 81 " model vdw 2.250 3.120 nonbonded pdb=" OD2 ASP A 113 " pdb=" NH2 ARG A 670 " model vdw 2.275 3.120 nonbonded pdb=" NH1 ARG L 24 " pdb=" OD1 ASP L 70 " model vdw 2.291 3.120 nonbonded pdb=" O ARG A 631 " pdb=" OG1 THR A 635 " model vdw 2.306 3.040 nonbonded pdb=" OG SER L 63 " pdb=" OG1 THR L 74 " model vdw 2.326 3.040 ... (remaining 34605 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.440 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: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.360 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 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 0.035 4468 Z= 0.147 Angle : 0.549 5.308 6090 Z= 0.285 Chirality : 0.043 0.132 673 Planarity : 0.004 0.035 778 Dihedral : 14.738 102.832 1684 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: 0.36 (0.39), residues: 529 helix: 1.64 (0.64), residues: 74 sheet: -0.09 (0.42), residues: 172 loop : 0.21 (0.39), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 13 TYR 0.012 0.002 TYR H 60 PHE 0.007 0.001 PHE A 630 TRP 0.015 0.001 TRP L 96 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 4462) covalent geometry : angle 0.54612 ( 6075) SS BOND : bond 0.00443 ( 3) SS BOND : angle 1.35921 ( 6) hydrogen bonds : bond 0.22832 ( 151) hydrogen bonds : angle 7.68776 ( 387) link_BETA1-4 : bond 0.00530 ( 1) link_BETA1-4 : angle 1.14571 ( 3) link_NAG-ASN : bond 0.00121 ( 2) link_NAG-ASN : angle 1.30956 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.214 Fit side-chains REVERT: H 10 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8212 (mm-30) REVERT: H 89 GLU cc_start: 0.8557 (tp30) cc_final: 0.8280 (tp30) REVERT: L 17 ASP cc_start: 0.8687 (t0) cc_final: 0.8397 (t0) REVERT: A 62 LYS cc_start: 0.9149 (tttt) cc_final: 0.8917 (ttpp) REVERT: A 662 ASN cc_start: 0.8339 (p0) cc_final: 0.7994 (p0) outliers start: 0 outliers final: 1 residues processed: 79 average time/residue: 0.7447 time to fit residues: 60.2246 Evaluate side-chains 46 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.0970 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.096785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.073205 restraints weight = 8128.035| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.34 r_work: 0.2808 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 4468 Z= 0.214 Angle : 0.642 6.258 6090 Z= 0.326 Chirality : 0.046 0.190 673 Planarity : 0.005 0.057 778 Dihedral : 9.897 78.522 657 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.05 % Allowed : 8.58 % Favored : 90.38 % 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: 0.31 (0.38), residues: 529 helix: 1.26 (0.59), residues: 81 sheet: -0.00 (0.43), residues: 160 loop : 0.15 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 676 TYR 0.025 0.002 TYR H 99 PHE 0.010 0.001 PHE L 98 TRP 0.014 0.001 TRP L 96 HIS 0.004 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 4462) covalent geometry : angle 0.63696 ( 6075) SS BOND : bond 0.00709 ( 3) SS BOND : angle 1.89538 ( 6) hydrogen bonds : bond 0.04609 ( 151) hydrogen bonds : angle 5.56863 ( 387) link_BETA1-4 : bond 0.00667 ( 1) link_BETA1-4 : angle 1.48462 ( 3) link_NAG-ASN : bond 0.00056 ( 2) link_NAG-ASN : angle 1.65348 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8168 (tp40) REVERT: H 10 GLU cc_start: 0.8573 (mm-30) cc_final: 0.7988 (mm-30) REVERT: H 43 GLN cc_start: 0.8696 (mp10) cc_final: 0.8397 (mm110) REVERT: H 59 ARG cc_start: 0.8107 (ppp80) cc_final: 0.7884 (ppp80) REVERT: H 89 GLU cc_start: 0.8729 (tp30) cc_final: 0.8422 (tp30) REVERT: L 24 ARG cc_start: 0.8272 (ttm-80) cc_final: 0.7622 (ttm-80) REVERT: A 107 LYS cc_start: 0.8697 (pptt) cc_final: 0.8492 (pptt) REVERT: A 108 ASN cc_start: 0.8658 (m-40) cc_final: 0.8321 (m-40) REVERT: A 662 ASN cc_start: 0.8458 (p0) cc_final: 0.7950 (p0) outliers start: 5 outliers final: 1 residues processed: 56 average time/residue: 0.6408 time to fit residues: 37.0441 Evaluate side-chains 45 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 99 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 44 optimal weight: 0.9990 chunk 43 optimal weight: 0.0060 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.1980 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 = 0.3363 r_free = 0.3363 target = 0.097676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.074154 restraints weight = 8019.170| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.34 r_work: 0.2817 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4468 Z= 0.154 Angle : 0.587 6.884 6090 Z= 0.295 Chirality : 0.044 0.151 673 Planarity : 0.004 0.043 778 Dihedral : 6.995 52.686 654 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.05 % Allowed : 10.04 % Favored : 88.91 % 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: 0.23 (0.38), residues: 529 helix: 1.50 (0.61), residues: 75 sheet: -0.23 (0.41), residues: 169 loop : 0.16 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 676 TYR 0.024 0.001 TYR H 99 PHE 0.007 0.001 PHE L 98 TRP 0.012 0.001 TRP L 96 HIS 0.003 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 4462) covalent geometry : angle 0.58277 ( 6075) SS BOND : bond 0.00499 ( 3) SS BOND : angle 1.54737 ( 6) hydrogen bonds : bond 0.03772 ( 151) hydrogen bonds : angle 5.16524 ( 387) link_BETA1-4 : bond 0.00524 ( 1) link_BETA1-4 : angle 1.41663 ( 3) link_NAG-ASN : bond 0.00067 ( 2) link_NAG-ASN : angle 1.64264 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8116 (tp40) REVERT: H 10 GLU cc_start: 0.8578 (mm-30) cc_final: 0.7976 (mm-30) REVERT: H 11 LEU cc_start: 0.9351 (tt) cc_final: 0.9109 (tm) REVERT: H 40 ARG cc_start: 0.8137 (mtm-85) cc_final: 0.7875 (mmm-85) REVERT: H 43 GLN cc_start: 0.8649 (mp10) cc_final: 0.8261 (mm110) REVERT: H 59 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7740 (ppp80) REVERT: L 17 ASP cc_start: 0.8762 (t0) cc_final: 0.8491 (t0) REVERT: L 24 ARG cc_start: 0.8242 (ttm-80) cc_final: 0.7735 (ttm-80) REVERT: L 70 ASP cc_start: 0.8356 (m-30) cc_final: 0.8058 (m-30) REVERT: A 107 LYS cc_start: 0.8740 (pptt) cc_final: 0.8500 (pptt) REVERT: A 108 ASN cc_start: 0.8594 (m-40) cc_final: 0.8198 (m-40) REVERT: A 662 ASN cc_start: 0.8465 (p0) cc_final: 0.7910 (p0) outliers start: 5 outliers final: 1 residues processed: 51 average time/residue: 0.7723 time to fit residues: 40.4971 Evaluate side-chains 48 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain H residue 99 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 32 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.095382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.071877 restraints weight = 7946.933| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.27 r_work: 0.2785 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 4468 Z= 0.226 Angle : 0.620 6.421 6090 Z= 0.312 Chirality : 0.045 0.154 673 Planarity : 0.005 0.046 778 Dihedral : 5.595 33.055 654 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.26 % Allowed : 12.13 % Favored : 86.61 % 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: 0.18 (0.37), residues: 529 helix: 1.34 (0.60), residues: 75 sheet: -0.09 (0.42), residues: 161 loop : 0.03 (0.38), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 676 TYR 0.025 0.002 TYR H 99 PHE 0.007 0.001 PHE A 247 TRP 0.014 0.001 TRP L 96 HIS 0.003 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00546 ( 4462) covalent geometry : angle 0.61532 ( 6075) SS BOND : bond 0.00577 ( 3) SS BOND : angle 1.67952 ( 6) hydrogen bonds : bond 0.03837 ( 151) hydrogen bonds : angle 5.06721 ( 387) link_BETA1-4 : bond 0.00476 ( 1) link_BETA1-4 : angle 1.39834 ( 3) link_NAG-ASN : bond 0.00476 ( 2) link_NAG-ASN : angle 1.76594 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8481 (mm-40) cc_final: 0.8127 (tp40) REVERT: H 10 GLU cc_start: 0.8602 (mm-30) cc_final: 0.7971 (mm-30) REVERT: H 11 LEU cc_start: 0.9356 (tt) cc_final: 0.9133 (tm) REVERT: H 31 ASP cc_start: 0.8649 (m-30) cc_final: 0.8397 (m-30) REVERT: H 43 GLN cc_start: 0.8718 (mp10) cc_final: 0.8515 (mp10) REVERT: H 59 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7729 (ppp80) REVERT: H 89 GLU cc_start: 0.8537 (tt0) cc_final: 0.8289 (tp30) REVERT: L 17 ASP cc_start: 0.8821 (t0) cc_final: 0.8549 (t0) REVERT: A 107 LYS cc_start: 0.8747 (pptt) cc_final: 0.8473 (pptt) REVERT: A 108 ASN cc_start: 0.8633 (m-40) cc_final: 0.8189 (m-40) REVERT: A 662 ASN cc_start: 0.8542 (p0) cc_final: 0.7948 (p0) outliers start: 6 outliers final: 3 residues processed: 54 average time/residue: 0.6088 time to fit residues: 33.8488 Evaluate side-chains 49 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 114 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 30 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 0.0050 chunk 17 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 3 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.0570 chunk 26 optimal weight: 0.5980 overall best weight: 0.3112 ------------------------------------------------------------------------------- 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 = 0.3357 r_free = 0.3357 target = 0.097877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.074613 restraints weight = 8057.313| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.32 r_work: 0.2826 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4468 Z= 0.123 Angle : 0.565 6.437 6090 Z= 0.286 Chirality : 0.043 0.169 673 Planarity : 0.004 0.056 778 Dihedral : 5.091 27.756 654 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.46 % Allowed : 12.34 % Favored : 86.19 % 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: 0.18 (0.38), residues: 529 helix: 1.55 (0.61), residues: 75 sheet: -0.29 (0.41), residues: 169 loop : 0.13 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 676 TYR 0.022 0.001 TYR H 99 PHE 0.013 0.001 PHE A 630 TRP 0.012 0.001 TRP L 96 HIS 0.003 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 4462) covalent geometry : angle 0.55932 ( 6075) SS BOND : bond 0.00404 ( 3) SS BOND : angle 1.43936 ( 6) hydrogen bonds : bond 0.03125 ( 151) hydrogen bonds : angle 4.87454 ( 387) link_BETA1-4 : bond 0.00423 ( 1) link_BETA1-4 : angle 1.32247 ( 3) link_NAG-ASN : bond 0.00361 ( 2) link_NAG-ASN : angle 1.94028 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8104 (tp40) REVERT: H 10 GLU cc_start: 0.8576 (mm-30) cc_final: 0.7949 (mm-30) REVERT: H 31 ASP cc_start: 0.8620 (m-30) cc_final: 0.8378 (m-30) REVERT: L 17 ASP cc_start: 0.8781 (t0) cc_final: 0.8463 (t0) REVERT: A 107 LYS cc_start: 0.8678 (pptt) cc_final: 0.8342 (pptt) REVERT: A 662 ASN cc_start: 0.8499 (p0) cc_final: 0.7856 (p0) REVERT: A 676 ARG cc_start: 0.8315 (mtm110) cc_final: 0.8058 (ptp-110) outliers start: 7 outliers final: 2 residues processed: 54 average time/residue: 0.5398 time to fit residues: 29.9720 Evaluate side-chains 47 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain A residue 69 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.0470 chunk 1 optimal weight: 0.3980 chunk 50 optimal weight: 0.0980 chunk 44 optimal weight: 0.0870 chunk 46 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 45 optimal weight: 0.0030 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.1266 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.099036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.075759 restraints weight = 8075.429| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.32 r_work: 0.2836 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4468 Z= 0.096 Angle : 0.548 6.800 6090 Z= 0.275 Chirality : 0.042 0.135 673 Planarity : 0.004 0.042 778 Dihedral : 4.617 22.284 654 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.84 % Allowed : 14.85 % Favored : 84.31 % 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: 0.30 (0.38), residues: 529 helix: 1.77 (0.62), residues: 75 sheet: -0.27 (0.42), residues: 168 loop : 0.21 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 676 TYR 0.020 0.001 TYR H 99 PHE 0.013 0.001 PHE A 630 TRP 0.012 0.001 TRP L 96 HIS 0.004 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 4462) covalent geometry : angle 0.54179 ( 6075) SS BOND : bond 0.00422 ( 3) SS BOND : angle 1.54149 ( 6) hydrogen bonds : bond 0.02736 ( 151) hydrogen bonds : angle 4.70080 ( 387) link_BETA1-4 : bond 0.00360 ( 1) link_BETA1-4 : angle 1.23512 ( 3) link_NAG-ASN : bond 0.00303 ( 2) link_NAG-ASN : angle 2.05322 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.105 Fit side-chains REVERT: H 5 GLN cc_start: 0.8373 (mm-40) cc_final: 0.8085 (tp40) REVERT: H 10 GLU cc_start: 0.8574 (mm-30) cc_final: 0.7936 (mm-30) REVERT: H 31 ASP cc_start: 0.8633 (m-30) cc_final: 0.8373 (m-30) REVERT: H 43 GLN cc_start: 0.8508 (mp10) cc_final: 0.8255 (mp10) REVERT: L 17 ASP cc_start: 0.8754 (t0) cc_final: 0.8417 (t0) REVERT: L 24 ARG cc_start: 0.8232 (ttm-80) cc_final: 0.7550 (ttm-80) REVERT: L 70 ASP cc_start: 0.8191 (m-30) cc_final: 0.7895 (m-30) REVERT: A 107 LYS cc_start: 0.8673 (pptt) cc_final: 0.8314 (pptt) REVERT: A 108 ASN cc_start: 0.8551 (m-40) cc_final: 0.7987 (m-40) REVERT: A 158 ARG cc_start: 0.8189 (tpm170) cc_final: 0.7964 (tpp-160) REVERT: A 662 ASN cc_start: 0.8523 (p0) cc_final: 0.7834 (p0) outliers start: 4 outliers final: 2 residues processed: 60 average time/residue: 0.5112 time to fit residues: 31.7182 Evaluate side-chains 51 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain A residue 69 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 45 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 4 optimal weight: 0.0970 chunk 31 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 46 optimal weight: 0.0670 chunk 17 optimal weight: 1.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- 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 = 0.3365 r_free = 0.3365 target = 0.098274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.075141 restraints weight = 8034.155| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.31 r_work: 0.2836 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4468 Z= 0.137 Angle : 0.568 6.051 6090 Z= 0.289 Chirality : 0.043 0.141 673 Planarity : 0.004 0.062 778 Dihedral : 4.509 19.231 654 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.26 % Allowed : 15.69 % Favored : 83.05 % 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: 0.31 (0.38), residues: 529 helix: 1.76 (0.62), residues: 75 sheet: -0.25 (0.42), residues: 169 loop : 0.21 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 676 TYR 0.024 0.001 TYR H 99 PHE 0.013 0.001 PHE A 630 TRP 0.013 0.001 TRP L 96 HIS 0.003 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 4462) covalent geometry : angle 0.56152 ( 6075) SS BOND : bond 0.00478 ( 3) SS BOND : angle 1.68193 ( 6) hydrogen bonds : bond 0.03016 ( 151) hydrogen bonds : angle 4.70260 ( 387) link_BETA1-4 : bond 0.00525 ( 1) link_BETA1-4 : angle 1.24292 ( 3) link_NAG-ASN : bond 0.00281 ( 2) link_NAG-ASN : angle 2.07844 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.104 Fit side-chains REVERT: H 5 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8068 (tp40) REVERT: H 10 GLU cc_start: 0.8558 (mm-30) cc_final: 0.7914 (mm-30) REVERT: H 13 ARG cc_start: 0.8305 (tpp-160) cc_final: 0.7772 (ttm-80) REVERT: H 31 ASP cc_start: 0.8546 (m-30) cc_final: 0.8314 (m-30) REVERT: H 43 GLN cc_start: 0.8572 (mp10) cc_final: 0.8240 (mp10) REVERT: L 17 ASP cc_start: 0.8775 (t0) cc_final: 0.8437 (t0) REVERT: L 24 ARG cc_start: 0.8233 (ttm-80) cc_final: 0.7588 (ttm-80) REVERT: L 70 ASP cc_start: 0.8255 (m-30) cc_final: 0.7944 (m-30) REVERT: A 107 LYS cc_start: 0.8700 (pptt) cc_final: 0.8331 (pptt) REVERT: A 108 ASN cc_start: 0.8604 (m-40) cc_final: 0.8011 (m-40) REVERT: A 662 ASN cc_start: 0.8598 (p0) cc_final: 0.7945 (p0) REVERT: A 676 ARG cc_start: 0.8309 (mtm110) cc_final: 0.8022 (ptp-110) outliers start: 6 outliers final: 3 residues processed: 53 average time/residue: 0.5081 time to fit residues: 27.8764 Evaluate side-chains 50 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 216 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 23 optimal weight: 0.0040 chunk 8 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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 = 0.3343 r_free = 0.3343 target = 0.096531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.074085 restraints weight = 7957.641| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.17 r_work: 0.2820 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4468 Z= 0.157 Angle : 0.585 7.656 6090 Z= 0.296 Chirality : 0.043 0.148 673 Planarity : 0.004 0.061 778 Dihedral : 4.481 19.471 654 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.46 % Allowed : 15.48 % Favored : 83.05 % 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: 0.26 (0.38), residues: 529 helix: 1.65 (0.63), residues: 75 sheet: -0.29 (0.42), residues: 169 loop : 0.20 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 676 TYR 0.025 0.002 TYR H 99 PHE 0.015 0.001 PHE A 630 TRP 0.013 0.001 TRP L 96 HIS 0.003 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 4462) covalent geometry : angle 0.57627 ( 6075) SS BOND : bond 0.00512 ( 3) SS BOND : angle 1.66062 ( 6) hydrogen bonds : bond 0.03115 ( 151) hydrogen bonds : angle 4.77075 ( 387) link_BETA1-4 : bond 0.00539 ( 1) link_BETA1-4 : angle 1.25123 ( 3) link_NAG-ASN : bond 0.00041 ( 2) link_NAG-ASN : angle 2.83584 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.171 Fit side-chains REVERT: H 5 GLN cc_start: 0.8414 (mm-40) cc_final: 0.8125 (tp40) REVERT: H 10 GLU cc_start: 0.8564 (mm-30) cc_final: 0.7879 (mm-30) REVERT: H 13 ARG cc_start: 0.8283 (tpp-160) cc_final: 0.7750 (ttm-80) REVERT: H 31 ASP cc_start: 0.8549 (m-30) cc_final: 0.8318 (m-30) REVERT: L 17 ASP cc_start: 0.8792 (t0) cc_final: 0.8463 (t0) REVERT: L 18 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8484 (ptm160) REVERT: L 24 ARG cc_start: 0.8261 (ttm-80) cc_final: 0.7634 (ttm-80) REVERT: L 70 ASP cc_start: 0.8314 (m-30) cc_final: 0.8010 (m-30) REVERT: A 107 LYS cc_start: 0.8696 (pptt) cc_final: 0.8323 (pptt) REVERT: A 108 ASN cc_start: 0.8614 (m-40) cc_final: 0.8055 (m-40) REVERT: A 662 ASN cc_start: 0.8595 (p0) cc_final: 0.7962 (p0) REVERT: A 676 ARG cc_start: 0.8308 (mtm110) cc_final: 0.8054 (ptp-110) outliers start: 7 outliers final: 4 residues processed: 52 average time/residue: 0.6030 time to fit residues: 32.3887 Evaluate side-chains 53 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 216 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.0010 chunk 45 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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 = 0.3340 r_free = 0.3340 target = 0.096490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.072963 restraints weight = 8029.749| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.30 r_work: 0.2808 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4468 Z= 0.174 Angle : 0.611 8.378 6090 Z= 0.306 Chirality : 0.044 0.142 673 Planarity : 0.005 0.053 778 Dihedral : 4.478 19.393 654 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.26 % Allowed : 15.69 % Favored : 83.05 % 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: 0.25 (0.38), residues: 529 helix: 1.62 (0.62), residues: 75 sheet: -0.30 (0.41), residues: 169 loop : 0.21 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 676 TYR 0.027 0.002 TYR H 99 PHE 0.015 0.001 PHE A 630 TRP 0.013 0.001 TRP L 96 HIS 0.003 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 4462) covalent geometry : angle 0.60425 ( 6075) SS BOND : bond 0.00498 ( 3) SS BOND : angle 1.74656 ( 6) hydrogen bonds : bond 0.03200 ( 151) hydrogen bonds : angle 4.80113 ( 387) link_BETA1-4 : bond 0.00483 ( 1) link_BETA1-4 : angle 1.22602 ( 3) link_NAG-ASN : bond 0.00388 ( 2) link_NAG-ASN : angle 2.39924 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.104 Fit side-chains REVERT: H 5 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8142 (tp40) REVERT: H 10 GLU cc_start: 0.8565 (mm-30) cc_final: 0.7926 (mm-30) REVERT: H 13 ARG cc_start: 0.8319 (tpp-160) cc_final: 0.7792 (ttm-80) REVERT: H 43 GLN cc_start: 0.8618 (mp10) cc_final: 0.8237 (mp10) REVERT: L 17 ASP cc_start: 0.8805 (t0) cc_final: 0.8463 (t0) REVERT: L 18 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8480 (ptm160) REVERT: A 107 LYS cc_start: 0.8741 (pptt) cc_final: 0.8324 (pptt) REVERT: A 108 ASN cc_start: 0.8628 (m-40) cc_final: 0.7997 (m-40) REVERT: A 662 ASN cc_start: 0.8621 (p0) cc_final: 0.8001 (p0) outliers start: 6 outliers final: 4 residues processed: 53 average time/residue: 0.5603 time to fit residues: 30.6464 Evaluate side-chains 51 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 216 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 27 optimal weight: 0.2980 chunk 22 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.097330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.074057 restraints weight = 8023.061| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.34 r_work: 0.2806 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4468 Z= 0.159 Angle : 0.627 11.064 6090 Z= 0.317 Chirality : 0.044 0.142 673 Planarity : 0.005 0.075 778 Dihedral : 4.448 20.403 654 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.26 % Allowed : 16.32 % Favored : 82.43 % 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: 0.27 (0.38), residues: 529 helix: 1.62 (0.62), residues: 75 sheet: -0.26 (0.41), residues: 168 loop : 0.20 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 676 TYR 0.027 0.002 TYR H 99 PHE 0.015 0.001 PHE A 630 TRP 0.012 0.001 TRP L 96 HIS 0.003 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 4462) covalent geometry : angle 0.62067 ( 6075) SS BOND : bond 0.00457 ( 3) SS BOND : angle 1.69409 ( 6) hydrogen bonds : bond 0.03132 ( 151) hydrogen bonds : angle 4.80612 ( 387) link_BETA1-4 : bond 0.00470 ( 1) link_BETA1-4 : angle 1.19706 ( 3) link_NAG-ASN : bond 0.00301 ( 2) link_NAG-ASN : angle 2.43924 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.174 Fit side-chains REVERT: H 5 GLN cc_start: 0.8407 (mm-40) cc_final: 0.8126 (tp40) REVERT: H 10 GLU cc_start: 0.8594 (mm-30) cc_final: 0.7950 (mm-30) REVERT: H 13 ARG cc_start: 0.8278 (tpp-160) cc_final: 0.7800 (ttm-80) REVERT: H 43 GLN cc_start: 0.8601 (mp10) cc_final: 0.8220 (mp10) REVERT: L 17 ASP cc_start: 0.8819 (t0) cc_final: 0.8474 (t0) REVERT: L 18 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8464 (ptm160) REVERT: L 24 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7798 (ttm-80) REVERT: A 107 LYS cc_start: 0.8735 (pptt) cc_final: 0.8322 (pptt) REVERT: A 108 ASN cc_start: 0.8570 (m-40) cc_final: 0.7954 (m-40) REVERT: A 190 ASP cc_start: 0.8296 (p0) cc_final: 0.8082 (p0) REVERT: A 662 ASN cc_start: 0.8616 (p0) cc_final: 0.7993 (p0) REVERT: A 676 ARG cc_start: 0.8236 (mtm110) cc_final: 0.7910 (ptp-110) outliers start: 6 outliers final: 5 residues processed: 53 average time/residue: 0.5675 time to fit residues: 31.1245 Evaluate side-chains 54 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 216 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 38 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 0.0060 chunk 4 optimal weight: 0.0870 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.0470 chunk 9 optimal weight: 0.6980 overall best weight: 0.2872 ------------------------------------------------------------------------------- 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 = 0.3369 r_free = 0.3369 target = 0.098541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.075300 restraints weight = 8050.018| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.33 r_work: 0.2829 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4468 Z= 0.122 Angle : 0.600 9.765 6090 Z= 0.307 Chirality : 0.043 0.137 673 Planarity : 0.005 0.074 778 Dihedral : 4.349 17.745 654 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.84 % Allowed : 16.95 % Favored : 82.22 % 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: 0.28 (0.38), residues: 529 helix: 1.70 (0.62), residues: 75 sheet: -0.26 (0.42), residues: 169 loop : 0.20 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 676 TYR 0.025 0.001 TYR H 99 PHE 0.015 0.001 PHE A 630 TRP 0.012 0.001 TRP L 96 HIS 0.003 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 4462) covalent geometry : angle 0.59346 ( 6075) SS BOND : bond 0.00509 ( 3) SS BOND : angle 1.59430 ( 6) hydrogen bonds : bond 0.02871 ( 151) hydrogen bonds : angle 4.70291 ( 387) link_BETA1-4 : bond 0.00450 ( 1) link_BETA1-4 : angle 1.16574 ( 3) link_NAG-ASN : bond 0.00271 ( 2) link_NAG-ASN : angle 2.40432 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1462.57 seconds wall clock time: 25 minutes 40.83 seconds (1540.83 seconds total)