Starting phenix.real_space_refine on Tue Feb 3 15:35:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9py6_72010/02_2026/9py6_72010.cif Found real_map, /net/cci-nas-00/data/ceres_data/9py6_72010/02_2026/9py6_72010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9py6_72010/02_2026/9py6_72010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9py6_72010/02_2026/9py6_72010.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9py6_72010/02_2026/9py6_72010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9py6_72010/02_2026/9py6_72010.map" } resolution = 2.9 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 8 5.16 5 C 2751 2.51 5 N 748 2.21 5 O 827 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 4334 Number of models: 1 Model: "" Number of chains: 4 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: "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: "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 Time building chain proxies: 0.77, per 1000 atoms: 0.18 Number of scatterers: 4334 At special positions: 0 Unit cell: (77.04, 98.44, 98.44, 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 827 8.00 N 748 7.00 C 2751 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 169 " distance=2.03 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 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 B 1 " - " ASN A 641 " Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 159.1 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 9 sheets defined 23.3% alpha, 32.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 110 through 132 removed outlier: 3.750A pdb=" N VAL A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Proline residue: A 118 - end of helix removed outlier: 3.980A pdb=" N ARG A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.758A pdb=" N GLU A 145 " --> pdb=" O SER A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 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 Processing helix chain 'A' and resid 244 through 259 Processing helix chain 'A' and resid 624 through 628 Processing helix chain 'A' and resid 631 through 639 removed outlier: 3.659A pdb=" N TYR A 639 " --> pdb=" O THR A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 669 removed outlier: 3.767A pdb=" N ALA A 666 " --> pdb=" O ASN A 662 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.706A 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: 3.605A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 60 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 60 removed outlier: 3.548A pdb=" N SER A 101 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 150 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.509A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY H 44 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.564A pdb=" N ARG H 98 " --> pdb=" O TYR H 109 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR H 109 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.253A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.857A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 171 hydrogen bonds defined for protein. 408 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: 0.62 Time building geometry restraints manager: 0.47 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: 1070 1.46 - 1.58: 1961 1.58 - 1.70: 0 1.70 - 1.81: 9 Bond restraints: 4448 Sorted by residual: bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.21e+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 1.10e+00 bond pdb=" C3 NAG B 2 " pdb=" O3 NAG B 2 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.02e+00 bond pdb=" C3 NAG B 1 " pdb=" O3 NAG B 1 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.73e-01 ... (remaining 4443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 5885 1.34 - 2.67: 130 2.67 - 4.01: 34 4.01 - 5.34: 6 5.34 - 6.68: 1 Bond angle restraints: 6056 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 113.90 117.86 -3.96 1.80e+00 3.09e-01 4.84e+00 angle pdb=" C GLY A 281 " pdb=" N ILE A 282 " pdb=" CA ILE A 282 " ideal model delta sigma weight residual 121.70 125.44 -3.74 1.80e+00 3.09e-01 4.31e+00 angle pdb=" CA PRO A 54 " pdb=" C PRO A 54 " pdb=" N VAL A 55 " ideal model delta sigma weight residual 114.74 116.85 -2.11 1.03e+00 9.43e-01 4.20e+00 angle pdb=" C GLY A 76 " pdb=" N GLU A 77 " pdb=" CA GLU A 77 " ideal model delta sigma weight residual 120.26 122.94 -2.68 1.34e+00 5.57e-01 4.00e+00 angle pdb=" C ASP A 113 " pdb=" N VAL A 114 " pdb=" CA VAL A 114 " ideal model delta sigma weight residual 120.47 123.59 -3.12 1.58e+00 4.01e-01 3.91e+00 ... (remaining 6051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 2490 17.04 - 34.07: 155 34.07 - 51.11: 23 51.11 - 68.14: 9 68.14 - 85.18: 5 Dihedral angle restraints: 2682 sinusoidal: 1114 harmonic: 1568 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 125.47 -32.47 1 1.00e+01 1.00e-02 1.50e+01 dihedral pdb=" CA ASN A 270 " pdb=" C ASN A 270 " pdb=" N LEU A 271 " pdb=" CA LEU A 271 " ideal model delta harmonic sigma weight residual 180.00 163.03 16.97 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ARG H 98 " pdb=" C ARG H 98 " pdb=" N TYR H 99 " pdb=" CA TYR H 99 " ideal model delta harmonic sigma weight residual 180.00 163.11 16.89 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 2679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 393 0.028 - 0.056: 165 0.056 - 0.084: 58 0.084 - 0.111: 38 0.111 - 0.139: 14 Chirality restraints: 668 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 641 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA VAL A 216 " pdb=" N VAL A 216 " pdb=" C VAL A 216 " pdb=" CB VAL A 216 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA VAL H 18 " pdb=" N VAL H 18 " pdb=" C VAL H 18 " pdb=" CB VAL H 18 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 665 not shown) Planarity restraints: 778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 59 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO A 60 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 60 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 60 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 188 " 0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO A 189 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 189 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 189 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 173 " -0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO A 174 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 174 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 174 " -0.016 5.00e-02 4.00e+02 ... (remaining 775 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1008 2.79 - 3.32: 3807 3.32 - 3.85: 6807 3.85 - 4.37: 8001 4.37 - 4.90: 14027 Nonbonded interactions: 33650 Sorted by model distance: nonbonded pdb=" O GLY A 87 " pdb=" OH TYR A 648 " model vdw 2.268 3.040 nonbonded pdb=" NH2 ARG A 246 " pdb=" O ASP H 31 " model vdw 2.301 3.120 nonbonded pdb=" OE2 GLU H 46 " pdb=" NZ LYS H 63 " model vdw 2.360 3.120 nonbonded pdb=" O ARG A 631 " pdb=" OG1 THR A 635 " model vdw 2.362 3.040 nonbonded pdb=" OG SER L 63 " pdb=" OG1 THR L 74 " model vdw 2.384 3.040 ... (remaining 33645 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.470 Find NCS groups from input model: 0.010 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:8.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 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 0.031 4453 Z= 0.126 Angle : 0.535 6.678 6068 Z= 0.282 Chirality : 0.042 0.139 668 Planarity : 0.004 0.030 777 Dihedral : 12.697 85.176 1663 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.38), residues: 529 helix: 1.51 (0.61), residues: 73 sheet: 0.54 (0.42), residues: 161 loop : 0.04 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 626 TYR 0.008 0.001 TYR H 102 PHE 0.006 0.001 PHE H 105 TRP 0.013 0.001 TRP L 96 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 4448) covalent geometry : angle 0.52947 ( 6056) SS BOND : bond 0.00323 ( 3) SS BOND : angle 0.38093 ( 6) hydrogen bonds : bond 0.20977 ( 150) hydrogen bonds : angle 7.66795 ( 408) link_BETA1-4 : bond 0.00345 ( 1) link_BETA1-4 : angle 2.45227 ( 3) link_NAG-ASN : bond 0.00026 ( 1) link_NAG-ASN : angle 2.62871 ( 3) *********************** 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 118 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.120 Fit side-chains REVERT: A 630 PHE cc_start: 0.7777 (p90) cc_final: 0.7509 (p90) REVERT: A 664 GLN cc_start: 0.8381 (mm110) cc_final: 0.7852 (mm-40) REVERT: H 19 LYS cc_start: 0.8858 (tttp) cc_final: 0.8593 (tttp) REVERT: H 67 LYS cc_start: 0.8397 (tppt) cc_final: 0.8187 (tppp) REVERT: H 73 ASP cc_start: 0.7827 (t0) cc_final: 0.7571 (t70) REVERT: H 82 GLN cc_start: 0.8019 (tt0) cc_final: 0.7696 (tp40) REVERT: H 90 ASP cc_start: 0.8484 (m-30) cc_final: 0.7299 (m-30) REVERT: L 53 ARG cc_start: 0.8237 (mmt90) cc_final: 0.8033 (mmm160) REVERT: L 61 ARG cc_start: 0.8392 (mtm-85) cc_final: 0.7830 (mtm-85) REVERT: L 82 ASP cc_start: 0.8519 (m-30) cc_final: 0.7746 (m-30) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.6498 time to fit residues: 78.6995 Evaluate side-chains 69 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 179 GLN A 638 ASN H 3 GLN H 55 ASN H 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.099486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.076470 restraints weight = 7628.242| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.87 r_work: 0.2902 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4453 Z= 0.182 Angle : 0.630 7.731 6068 Z= 0.318 Chirality : 0.045 0.169 668 Planarity : 0.005 0.038 777 Dihedral : 4.711 23.051 633 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.93 % Allowed : 10.88 % 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: 0.29 (0.37), residues: 529 helix: 1.14 (0.60), residues: 76 sheet: 0.36 (0.40), residues: 167 loop : -0.07 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 13 TYR 0.034 0.002 TYR H 99 PHE 0.011 0.001 PHE H 105 TRP 0.014 0.002 TRP L 96 HIS 0.004 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 4448) covalent geometry : angle 0.62172 ( 6056) SS BOND : bond 0.00831 ( 3) SS BOND : angle 1.16196 ( 6) hydrogen bonds : bond 0.04754 ( 150) hydrogen bonds : angle 5.49526 ( 408) link_BETA1-4 : bond 0.00433 ( 1) link_BETA1-4 : angle 3.46050 ( 3) link_NAG-ASN : bond 0.00360 ( 1) link_NAG-ASN : angle 3.01234 ( 3) *********************** 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 84 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.6990 (pmmt) REVERT: A 211 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8083 (m-30) REVERT: A 630 PHE cc_start: 0.8020 (p90) cc_final: 0.7544 (p90) REVERT: A 647 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8075 (mtm180) REVERT: H 67 LYS cc_start: 0.8488 (tppt) cc_final: 0.8234 (tppp) REVERT: H 82 GLN cc_start: 0.8112 (tt0) cc_final: 0.7701 (tp40) REVERT: H 86 LEU cc_start: 0.8332 (mm) cc_final: 0.7888 (mm) REVERT: H 90 ASP cc_start: 0.8180 (m-30) cc_final: 0.7493 (m-30) REVERT: L 3 GLN cc_start: 0.7987 (mp10) cc_final: 0.7605 (tt0) REVERT: L 61 ARG cc_start: 0.8397 (mtm-85) cc_final: 0.8189 (mtm-85) REVERT: L 77 ASN cc_start: 0.8263 (p0) cc_final: 0.8059 (p0) REVERT: L 82 ASP cc_start: 0.8483 (m-30) cc_final: 0.8082 (m-30) REVERT: L 103 LYS cc_start: 0.8516 (ttpp) cc_final: 0.8123 (tppp) outliers start: 14 outliers final: 6 residues processed: 81 average time/residue: 0.5325 time to fit residues: 44.5649 Evaluate side-chains 72 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 270 ASN H 3 GLN H 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.098333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.075470 restraints weight = 7582.276| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.84 r_work: 0.2883 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4453 Z= 0.206 Angle : 0.633 7.138 6068 Z= 0.317 Chirality : 0.045 0.155 668 Planarity : 0.005 0.037 777 Dihedral : 4.839 22.568 633 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.14 % Allowed : 12.76 % Favored : 84.10 % 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: 1.04 (0.60), residues: 76 sheet: 0.22 (0.39), residues: 168 loop : -0.10 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 13 TYR 0.031 0.002 TYR H 99 PHE 0.012 0.001 PHE H 105 TRP 0.014 0.002 TRP H 47 HIS 0.004 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 4448) covalent geometry : angle 0.62310 ( 6056) SS BOND : bond 0.01043 ( 3) SS BOND : angle 1.16967 ( 6) hydrogen bonds : bond 0.04136 ( 150) hydrogen bonds : angle 5.31700 ( 408) link_BETA1-4 : bond 0.00528 ( 1) link_BETA1-4 : angle 3.85121 ( 3) link_NAG-ASN : bond 0.00516 ( 1) link_NAG-ASN : angle 3.21698 ( 3) *********************** 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 80 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7009 (pmmt) REVERT: A 211 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8132 (m-30) REVERT: A 630 PHE cc_start: 0.8174 (p90) cc_final: 0.7688 (p90) REVERT: A 647 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8100 (mtm180) REVERT: A 668 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: H 10 GLU cc_start: 0.7904 (mp0) cc_final: 0.7498 (mp0) REVERT: H 19 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8627 (tttm) REVERT: H 39 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8102 (tt0) REVERT: H 67 LYS cc_start: 0.8504 (tppt) cc_final: 0.8255 (tppp) REVERT: H 82 GLN cc_start: 0.8218 (tt0) cc_final: 0.7743 (tp40) REVERT: H 86 LEU cc_start: 0.8294 (mm) cc_final: 0.7841 (mm) REVERT: H 90 ASP cc_start: 0.8219 (m-30) cc_final: 0.7758 (m-30) REVERT: L 1 ASP cc_start: 0.6506 (p0) cc_final: 0.6281 (p0) REVERT: L 3 GLN cc_start: 0.7655 (mp10) cc_final: 0.7448 (mp10) REVERT: L 18 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8008 (ptm160) REVERT: L 61 ARG cc_start: 0.8406 (mtm-85) cc_final: 0.8193 (mtm-85) REVERT: L 82 ASP cc_start: 0.8496 (m-30) cc_final: 0.8099 (m-30) outliers start: 15 outliers final: 6 residues processed: 76 average time/residue: 0.6099 time to fit residues: 47.7572 Evaluate side-chains 76 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 73 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 46 optimal weight: 2.9990 chunk 3 optimal weight: 0.0010 chunk 7 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN H 3 GLN L 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.100084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.077562 restraints weight = 7504.154| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.82 r_work: 0.2922 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4453 Z= 0.116 Angle : 0.564 6.468 6068 Z= 0.287 Chirality : 0.043 0.142 668 Planarity : 0.004 0.038 777 Dihedral : 4.594 22.199 633 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.14 % Allowed : 13.81 % 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: 0.19 (0.37), residues: 529 helix: 1.19 (0.61), residues: 76 sheet: 0.21 (0.39), residues: 167 loop : -0.13 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 13 TYR 0.024 0.001 TYR H 99 PHE 0.006 0.001 PHE L 98 TRP 0.011 0.001 TRP L 96 HIS 0.002 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 4448) covalent geometry : angle 0.55536 ( 6056) SS BOND : bond 0.00479 ( 3) SS BOND : angle 1.25884 ( 6) hydrogen bonds : bond 0.03165 ( 150) hydrogen bonds : angle 4.84669 ( 408) link_BETA1-4 : bond 0.00481 ( 1) link_BETA1-4 : angle 3.27068 ( 3) link_NAG-ASN : bond 0.00245 ( 1) link_NAG-ASN : angle 2.72071 ( 3) *********************** 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 79 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.6912 (pmmt) REVERT: A 211 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8056 (m-30) REVERT: A 241 GLN cc_start: 0.8719 (tt0) cc_final: 0.8495 (tp40) REVERT: A 630 PHE cc_start: 0.8104 (p90) cc_final: 0.7659 (p90) REVERT: A 647 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8101 (mtm180) REVERT: A 668 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: H 19 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8586 (tttm) REVERT: H 39 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8015 (tt0) REVERT: H 67 LYS cc_start: 0.8473 (tppt) cc_final: 0.8246 (tppp) REVERT: H 82 GLN cc_start: 0.8171 (tt0) cc_final: 0.7734 (tp40) REVERT: H 86 LEU cc_start: 0.8262 (mm) cc_final: 0.7776 (mm) REVERT: L 1 ASP cc_start: 0.6641 (p0) cc_final: 0.6355 (p0) REVERT: L 3 GLN cc_start: 0.7677 (mp10) cc_final: 0.7430 (mp10) REVERT: L 82 ASP cc_start: 0.8494 (m-30) cc_final: 0.8216 (m-30) REVERT: L 103 LYS cc_start: 0.8383 (ttpp) cc_final: 0.8177 (tppp) outliers start: 15 outliers final: 5 residues processed: 77 average time/residue: 0.6346 time to fit residues: 50.3725 Evaluate side-chains 70 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 41 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.0870 chunk 34 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN H 3 GLN H 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.100396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.077616 restraints weight = 7598.138| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.87 r_work: 0.2922 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4453 Z= 0.116 Angle : 0.562 7.160 6068 Z= 0.283 Chirality : 0.042 0.165 668 Planarity : 0.004 0.038 777 Dihedral : 4.502 22.295 633 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.35 % Allowed : 14.02 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.36), residues: 529 helix: 1.73 (0.63), residues: 70 sheet: 0.19 (0.39), residues: 167 loop : -0.08 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 13 TYR 0.023 0.001 TYR H 99 PHE 0.006 0.001 PHE L 98 TRP 0.012 0.001 TRP L 96 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4448) covalent geometry : angle 0.55247 ( 6056) SS BOND : bond 0.00566 ( 3) SS BOND : angle 1.63694 ( 6) hydrogen bonds : bond 0.03064 ( 150) hydrogen bonds : angle 4.71910 ( 408) link_BETA1-4 : bond 0.00496 ( 1) link_BETA1-4 : angle 3.28651 ( 3) link_NAG-ASN : bond 0.00237 ( 1) link_NAG-ASN : angle 2.57427 ( 3) *********************** 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 79 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.6916 (pmmt) REVERT: A 211 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8116 (m-30) REVERT: A 241 GLN cc_start: 0.8730 (tt0) cc_final: 0.8501 (tp-100) REVERT: A 630 PHE cc_start: 0.8095 (p90) cc_final: 0.7664 (p90) REVERT: A 647 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8121 (mtm180) REVERT: H 19 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8560 (tttm) REVERT: H 39 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: H 67 LYS cc_start: 0.8488 (tppt) cc_final: 0.8255 (tppp) REVERT: H 82 GLN cc_start: 0.8182 (tt0) cc_final: 0.7737 (tp40) REVERT: H 86 LEU cc_start: 0.8278 (mm) cc_final: 0.7793 (mm) REVERT: H 90 ASP cc_start: 0.8918 (m-30) cc_final: 0.8706 (m-30) REVERT: L 3 GLN cc_start: 0.7745 (mp10) cc_final: 0.7538 (tt0) REVERT: L 82 ASP cc_start: 0.8475 (m-30) cc_final: 0.8172 (m-30) outliers start: 16 outliers final: 7 residues processed: 77 average time/residue: 0.5598 time to fit residues: 44.4014 Evaluate side-chains 70 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 41 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 9 optimal weight: 0.0670 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.100759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.077884 restraints weight = 7632.145| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.88 r_work: 0.2932 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4453 Z= 0.117 Angle : 0.581 6.783 6068 Z= 0.293 Chirality : 0.042 0.154 668 Planarity : 0.004 0.041 777 Dihedral : 4.475 22.156 633 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.35 % Allowed : 15.90 % Favored : 80.75 % 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 (0.37), residues: 529 helix: 1.77 (0.63), residues: 70 sheet: 0.19 (0.38), residues: 167 loop : -0.02 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 13 TYR 0.023 0.001 TYR H 99 PHE 0.006 0.001 PHE L 98 TRP 0.012 0.001 TRP L 96 HIS 0.002 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 4448) covalent geometry : angle 0.57214 ( 6056) SS BOND : bond 0.00588 ( 3) SS BOND : angle 1.65974 ( 6) hydrogen bonds : bond 0.03085 ( 150) hydrogen bonds : angle 4.70763 ( 408) link_BETA1-4 : bond 0.00548 ( 1) link_BETA1-4 : angle 3.19652 ( 3) link_NAG-ASN : bond 0.00201 ( 1) link_NAG-ASN : angle 2.47937 ( 3) *********************** 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 77 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 64 TYR cc_start: 0.8273 (t80) cc_final: 0.8030 (t80) REVERT: A 107 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.6894 (pmmt) REVERT: A 211 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.8092 (m-30) REVERT: A 241 GLN cc_start: 0.8728 (tt0) cc_final: 0.8513 (tp-100) REVERT: A 630 PHE cc_start: 0.8076 (p90) cc_final: 0.7655 (p90) REVERT: A 647 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8063 (mtm180) REVERT: H 19 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8558 (tttm) REVERT: H 39 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8017 (tt0) REVERT: H 67 LYS cc_start: 0.8480 (tppt) cc_final: 0.8246 (tppp) REVERT: H 82 GLN cc_start: 0.8192 (tt0) cc_final: 0.7768 (tp40) REVERT: H 86 LEU cc_start: 0.8328 (mm) cc_final: 0.7826 (mm) REVERT: L 82 ASP cc_start: 0.8475 (m-30) cc_final: 0.8244 (m-30) outliers start: 16 outliers final: 7 residues processed: 74 average time/residue: 0.5381 time to fit residues: 41.0917 Evaluate side-chains 70 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.0770 chunk 42 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN H 3 GLN H 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.100627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.077758 restraints weight = 7609.470| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.87 r_work: 0.2928 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 4453 Z= 0.127 Angle : 0.596 6.713 6068 Z= 0.305 Chirality : 0.043 0.150 668 Planarity : 0.004 0.043 777 Dihedral : 4.403 22.255 633 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.77 % Allowed : 15.69 % Favored : 80.54 % 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: 0.36 (0.37), residues: 529 helix: 1.76 (0.63), residues: 70 sheet: 0.19 (0.38), residues: 167 loop : -0.02 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 13 TYR 0.024 0.001 TYR H 99 PHE 0.006 0.001 PHE L 98 TRP 0.011 0.001 TRP L 96 HIS 0.003 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 4448) covalent geometry : angle 0.58324 ( 6056) SS BOND : bond 0.00655 ( 3) SS BOND : angle 2.87188 ( 6) hydrogen bonds : bond 0.03156 ( 150) hydrogen bonds : angle 4.70523 ( 408) link_BETA1-4 : bond 0.00518 ( 1) link_BETA1-4 : angle 3.19256 ( 3) link_NAG-ASN : bond 0.00250 ( 1) link_NAG-ASN : angle 2.46521 ( 3) *********************** 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 76 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 64 TYR cc_start: 0.8239 (t80) cc_final: 0.8001 (t80) REVERT: A 107 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.6907 (pmmt) REVERT: A 211 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8120 (m-30) REVERT: A 630 PHE cc_start: 0.8081 (p90) cc_final: 0.7663 (p90) REVERT: A 647 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8111 (mtm180) REVERT: H 19 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8559 (tttm) REVERT: H 39 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: H 67 LYS cc_start: 0.8471 (tppt) cc_final: 0.8234 (tppp) REVERT: H 82 GLN cc_start: 0.8187 (tt0) cc_final: 0.7752 (tp40) REVERT: H 86 LEU cc_start: 0.8325 (mm) cc_final: 0.7813 (mm) REVERT: L 18 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7749 (ptm160) REVERT: L 105 GLU cc_start: 0.7712 (pt0) cc_final: 0.7342 (pm20) outliers start: 18 outliers final: 8 residues processed: 71 average time/residue: 0.5340 time to fit residues: 39.0631 Evaluate side-chains 72 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 107 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 0.0170 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.100802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.078079 restraints weight = 7569.762| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.87 r_work: 0.2933 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4453 Z= 0.121 Angle : 0.597 7.224 6068 Z= 0.304 Chirality : 0.043 0.147 668 Planarity : 0.004 0.047 777 Dihedral : 4.379 22.284 633 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.35 % Allowed : 15.69 % Favored : 80.96 % 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: 0.39 (0.37), residues: 529 helix: 1.72 (0.62), residues: 70 sheet: 0.31 (0.39), residues: 159 loop : -0.04 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 13 TYR 0.024 0.001 TYR H 99 PHE 0.006 0.001 PHE L 87 TRP 0.012 0.001 TRP L 96 HIS 0.002 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 4448) covalent geometry : angle 0.58295 ( 6056) SS BOND : bond 0.00604 ( 3) SS BOND : angle 3.18167 ( 6) hydrogen bonds : bond 0.03131 ( 150) hydrogen bonds : angle 4.65732 ( 408) link_BETA1-4 : bond 0.00510 ( 1) link_BETA1-4 : angle 3.13980 ( 3) link_NAG-ASN : bond 0.00212 ( 1) link_NAG-ASN : angle 2.41198 ( 3) *********************** 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 78 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 64 TYR cc_start: 0.8266 (t80) cc_final: 0.8046 (t80) REVERT: A 107 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.6890 (pmmt) REVERT: A 211 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8075 (m-30) REVERT: A 241 GLN cc_start: 0.8741 (tt0) cc_final: 0.8516 (tp-100) REVERT: A 630 PHE cc_start: 0.8101 (p90) cc_final: 0.7690 (p90) REVERT: A 647 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8076 (mtm180) REVERT: H 19 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8565 (tttm) REVERT: H 39 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8026 (tt0) REVERT: H 67 LYS cc_start: 0.8478 (tppt) cc_final: 0.8249 (tppp) REVERT: H 71 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8260 (p) REVERT: H 82 GLN cc_start: 0.8194 (tt0) cc_final: 0.7771 (tp40) REVERT: H 86 LEU cc_start: 0.8341 (mm) cc_final: 0.7827 (mm) REVERT: L 105 GLU cc_start: 0.7792 (pt0) cc_final: 0.7337 (pm20) outliers start: 16 outliers final: 8 residues processed: 73 average time/residue: 0.5266 time to fit residues: 39.7308 Evaluate side-chains 72 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 47 optimal weight: 0.0670 chunk 35 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 31 optimal weight: 0.0770 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.101785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.078972 restraints weight = 7681.557| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.86 r_work: 0.2949 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4453 Z= 0.111 Angle : 0.580 6.491 6068 Z= 0.296 Chirality : 0.042 0.143 668 Planarity : 0.004 0.049 777 Dihedral : 4.332 22.213 633 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.93 % Allowed : 16.32 % Favored : 80.75 % 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: 0.49 (0.37), residues: 529 helix: 1.77 (0.62), residues: 70 sheet: 0.30 (0.39), residues: 159 loop : 0.09 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 13 TYR 0.023 0.001 TYR H 99 PHE 0.006 0.001 PHE L 98 TRP 0.011 0.001 TRP L 96 HIS 0.002 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 4448) covalent geometry : angle 0.56878 ( 6056) SS BOND : bond 0.00640 ( 3) SS BOND : angle 2.46430 ( 6) hydrogen bonds : bond 0.02928 ( 150) hydrogen bonds : angle 4.61326 ( 408) link_BETA1-4 : bond 0.00490 ( 1) link_BETA1-4 : angle 2.97773 ( 3) link_NAG-ASN : bond 0.00199 ( 1) link_NAG-ASN : angle 2.31281 ( 3) *********************** 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 78 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: A 64 TYR cc_start: 0.8240 (t80) cc_final: 0.7979 (t80) REVERT: A 107 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.6899 (pmmt) REVERT: A 211 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: A 241 GLN cc_start: 0.8667 (tt0) cc_final: 0.8458 (tp-100) REVERT: A 630 PHE cc_start: 0.8017 (p90) cc_final: 0.7685 (p90) REVERT: H 19 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8556 (tttm) REVERT: H 39 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: H 40 ARG cc_start: 0.7814 (mmm-85) cc_final: 0.7608 (mmm-85) REVERT: H 71 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8263 (p) REVERT: H 82 GLN cc_start: 0.8180 (tt0) cc_final: 0.7783 (tp40) REVERT: H 86 LEU cc_start: 0.8353 (mm) cc_final: 0.7881 (mm) REVERT: L 82 ASP cc_start: 0.8484 (m-30) cc_final: 0.8250 (m-30) REVERT: L 105 GLU cc_start: 0.7791 (pt0) cc_final: 0.7298 (pm20) outliers start: 14 outliers final: 6 residues processed: 75 average time/residue: 0.5665 time to fit residues: 43.8114 Evaluate side-chains 71 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 0.1980 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.101700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.080085 restraints weight = 7552.822| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.74 r_work: 0.2952 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4453 Z= 0.115 Angle : 0.584 6.455 6068 Z= 0.300 Chirality : 0.042 0.142 668 Planarity : 0.004 0.038 777 Dihedral : 4.318 22.244 633 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.72 % Allowed : 16.32 % Favored : 80.96 % 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: 0.52 (0.37), residues: 529 helix: 1.80 (0.62), residues: 70 sheet: 0.23 (0.39), residues: 161 loop : 0.17 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 61 TYR 0.023 0.001 TYR H 99 PHE 0.009 0.001 PHE L 87 TRP 0.012 0.001 TRP L 96 HIS 0.002 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4448) covalent geometry : angle 0.57325 ( 6056) SS BOND : bond 0.00513 ( 3) SS BOND : angle 2.56209 ( 6) hydrogen bonds : bond 0.02958 ( 150) hydrogen bonds : angle 4.55684 ( 408) link_BETA1-4 : bond 0.00508 ( 1) link_BETA1-4 : angle 2.92950 ( 3) link_NAG-ASN : bond 0.00186 ( 1) link_NAG-ASN : angle 2.25199 ( 3) ********************** 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 72 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 64 TYR cc_start: 0.8315 (t80) cc_final: 0.8027 (t80) REVERT: A 107 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.6935 (pmmt) REVERT: A 211 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8260 (m-30) REVERT: A 241 GLN cc_start: 0.8854 (tt0) cc_final: 0.8618 (tp-100) REVERT: A 630 PHE cc_start: 0.8105 (p90) cc_final: 0.7782 (p90) REVERT: A 647 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8193 (mtm180) REVERT: H 13 ARG cc_start: 0.8359 (tpp-160) cc_final: 0.8034 (ttm110) REVERT: H 19 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8583 (tttm) REVERT: H 39 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8136 (tt0) REVERT: H 40 ARG cc_start: 0.7877 (mmm-85) cc_final: 0.7563 (mmm-85) REVERT: H 71 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8331 (p) REVERT: H 82 GLN cc_start: 0.8314 (tt0) cc_final: 0.7923 (tp40) REVERT: H 86 LEU cc_start: 0.8432 (mm) cc_final: 0.7919 (mm) REVERT: L 81 GLU cc_start: 0.8602 (pm20) cc_final: 0.8098 (pp20) REVERT: L 82 ASP cc_start: 0.8661 (m-30) cc_final: 0.8238 (m-30) REVERT: L 105 GLU cc_start: 0.7902 (pt0) cc_final: 0.7393 (pm20) outliers start: 13 outliers final: 6 residues processed: 70 average time/residue: 0.6258 time to fit residues: 45.1850 Evaluate side-chains 69 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.100198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.078109 restraints weight = 7636.048| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.79 r_work: 0.2928 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4453 Z= 0.137 Angle : 0.601 6.608 6068 Z= 0.306 Chirality : 0.043 0.143 668 Planarity : 0.004 0.038 777 Dihedral : 4.428 22.617 633 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.35 % Allowed : 16.32 % Favored : 80.33 % 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: 0.48 (0.37), residues: 529 helix: 1.70 (0.62), residues: 70 sheet: 0.22 (0.39), residues: 161 loop : 0.14 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 61 TYR 0.025 0.001 TYR H 99 PHE 0.007 0.001 PHE H 105 TRP 0.012 0.001 TRP L 96 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 4448) covalent geometry : angle 0.58809 ( 6056) SS BOND : bond 0.00712 ( 3) SS BOND : angle 2.77643 ( 6) hydrogen bonds : bond 0.03127 ( 150) hydrogen bonds : angle 4.63605 ( 408) link_BETA1-4 : bond 0.00509 ( 1) link_BETA1-4 : angle 3.17558 ( 3) link_NAG-ASN : bond 0.00241 ( 1) link_NAG-ASN : angle 2.40306 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1488.45 seconds wall clock time: 26 minutes 2.11 seconds (1562.11 seconds total)