Starting phenix.real_space_refine on Wed Sep 17 20:20:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ge8_51293/09_2025/9ge8_51293.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ge8_51293/09_2025/9ge8_51293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ge8_51293/09_2025/9ge8_51293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ge8_51293/09_2025/9ge8_51293.map" model { file = "/net/cci-nas-00/data/ceres_data/9ge8_51293/09_2025/9ge8_51293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ge8_51293/09_2025/9ge8_51293.cif" } resolution = 4.55 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 7086 2.51 5 N 1962 2.21 5 O 2027 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11130 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6295 Classifications: {'peptide': 804} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 40, 'TRANS': 760} Chain: "B" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1702 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain: "C" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1702 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain: "T" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1367 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 12, 'TRANS': 159} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.86, per 1000 atoms: 0.26 Number of scatterers: 11130 At special positions: 0 Unit cell: (116.065, 92.685, 156.145, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 6 15.00 Mg 2 11.99 O 2027 8.00 N 1962 7.00 C 7086 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 558.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2620 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 9 sheets defined 56.5% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 3.761A pdb=" N ARG A 11 " --> pdb=" O TRP A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 52 Processing helix chain 'A' and resid 64 through 75 removed outlier: 4.268A pdb=" N LEU A 68 " --> pdb=" O PRO A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.581A pdb=" N THR A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 231 through 270 Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 283 through 322 Processing helix chain 'A' and resid 334 through 362 removed outlier: 4.639A pdb=" N ARG A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Proline residue: A 355 - end of helix Processing helix chain 'A' and resid 363 through 369 Processing helix chain 'A' and resid 378 through 399 Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 401 through 431 Processing helix chain 'A' and resid 436 through 449 removed outlier: 3.939A pdb=" N GLN A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 485 removed outlier: 3.562A pdb=" N THR A 453 " --> pdb=" O GLN A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 512 removed outlier: 4.629A pdb=" N ALA A 503 " --> pdb=" O THR A 499 " (cutoff:3.500A) Proline residue: A 504 - end of helix Processing helix chain 'A' and resid 540 through 544 Processing helix chain 'A' and resid 577 through 583 Processing helix chain 'A' and resid 645 through 655 Processing helix chain 'A' and resid 663 through 707 Processing helix chain 'A' and resid 707 through 718 Processing helix chain 'A' and resid 720 through 758 removed outlier: 3.812A pdb=" N ILE A 745 " --> pdb=" O LEU A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 794 removed outlier: 3.593A pdb=" N TRP A 770 " --> pdb=" O ASP A 766 " (cutoff:3.500A) Proline residue: A 774 - end of helix removed outlier: 3.644A pdb=" N LYS A 794 " --> pdb=" O ALA A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 802 Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 48 through 57 Processing helix chain 'B' and resid 78 through 89 Processing helix chain 'B' and resid 104 through 116 Proline residue: B 112 - end of helix Processing helix chain 'B' and resid 119 through 134 Processing helix chain 'B' and resid 148 through 164 Processing helix chain 'B' and resid 178 through 197 Processing helix chain 'B' and resid 206 through 213 Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 78 through 89 Processing helix chain 'C' and resid 104 through 116 Proline residue: C 112 - end of helix Processing helix chain 'C' and resid 119 through 134 Processing helix chain 'C' and resid 148 through 164 Processing helix chain 'C' and resid 178 through 197 Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'T' and resid 35 through 40 Processing helix chain 'T' and resid 48 through 57 Processing helix chain 'T' and resid 72 through 88 Proline residue: T 81 - end of helix Processing helix chain 'T' and resid 97 through 104 Processing helix chain 'T' and resid 106 through 124 Processing helix chain 'T' and resid 136 through 139 Processing helix chain 'T' and resid 140 through 149 Processing helix chain 'T' and resid 149 through 159 removed outlier: 3.723A pdb=" N LYS T 153 " --> pdb=" O ALA T 149 " (cutoff:3.500A) Processing helix chain 'T' and resid 167 through 172 removed outlier: 3.870A pdb=" N LEU T 172 " --> pdb=" O GLU T 168 " (cutoff:3.500A) Processing helix chain 'T' and resid 173 through 177 Processing helix chain 'T' and resid 187 through 199 removed outlier: 4.335A pdb=" N PHE T 191 " --> pdb=" O ASP T 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 59 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 55 through 59 current: chain 'A' and resid 93 through 102 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 93 through 102 current: chain 'A' and resid 149 through 159 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 492 through 497 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 492 through 497 current: chain 'A' and resid 533 through 534 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 533 through 534 current: chain 'A' and resid 598 through 608 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 31 through 34 removed outlier: 5.519A pdb=" N VAL B 9 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N SER B 68 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N HIS B 11 " --> pdb=" O GLU B 66 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLU B 66 " --> pdb=" O HIS B 11 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 15 through 16 Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 93 removed outlier: 6.278A pdb=" N GLY B 91 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ASP B 171 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL B 93 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE B 39 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N THR B 38 " --> pdb=" O ARG B 215 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU B 217 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA B 40 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LEU B 219 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL B 42 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N CYS B 216 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 31 through 34 removed outlier: 5.518A pdb=" N VAL C 9 " --> pdb=" O SER C 68 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N SER C 68 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N HIS C 11 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLU C 66 " --> pdb=" O HIS C 11 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 15 through 16 Processing sheet with id=AA8, first strand: chain 'C' and resid 90 through 93 removed outlier: 6.279A pdb=" N GLY C 91 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ASP C 171 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL C 93 " --> pdb=" O ASP C 171 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE C 39 " --> pdb=" O MET C 202 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N THR C 38 " --> pdb=" O ARG C 215 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU C 217 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA C 40 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU C 219 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL C 42 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N CYS C 216 " --> pdb=" O GLU C 227 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'T' and resid 62 through 65 removed outlier: 6.074A pdb=" N LEU T 30 " --> pdb=" O VAL T 64 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR T 29 " --> pdb=" O TRP T 91 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU T 93 " --> pdb=" O THR T 29 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU T 31 " --> pdb=" O LEU T 93 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET T 131 " --> pdb=" O VAL T 94 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N LEU T 163 " --> pdb=" O PRO T 128 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU T 130 " --> pdb=" O LEU T 163 " (cutoff:3.500A) 607 hydrogen bonds defined for protein. 1761 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: 1.68 Time building geometry restraints manager: 1.26 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: 3722 1.34 - 1.46: 2139 1.46 - 1.58: 5392 1.58 - 1.69: 6 1.69 - 1.81: 88 Bond restraints: 11347 Sorted by residual: bond pdb=" CA GLU T 95 " pdb=" CB GLU T 95 " ideal model delta sigma weight residual 1.527 1.557 -0.030 2.48e-02 1.63e+03 1.47e+00 bond pdb=" CB PRO C 165 " pdb=" CG PRO C 165 " ideal model delta sigma weight residual 1.492 1.539 -0.047 5.00e-02 4.00e+02 8.83e-01 bond pdb=" CB PRO B 165 " pdb=" CG PRO B 165 " ideal model delta sigma weight residual 1.492 1.539 -0.047 5.00e-02 4.00e+02 8.81e-01 bond pdb=" CA VAL A 187 " pdb=" CB VAL A 187 " ideal model delta sigma weight residual 1.530 1.539 -0.008 1.05e-02 9.07e+03 6.24e-01 bond pdb=" CB GLU T 95 " pdb=" CG GLU T 95 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 4.79e-01 ... (remaining 11342 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 15147 1.29 - 2.57: 197 2.57 - 3.86: 43 3.86 - 5.15: 20 5.15 - 6.43: 9 Bond angle restraints: 15416 Sorted by residual: angle pdb=" C SER C 96 " pdb=" N PHE C 97 " pdb=" CA PHE C 97 " ideal model delta sigma weight residual 121.54 125.72 -4.18 1.91e+00 2.74e-01 4.79e+00 angle pdb=" C SER B 96 " pdb=" N PHE B 97 " pdb=" CA PHE B 97 " ideal model delta sigma weight residual 121.54 125.70 -4.16 1.91e+00 2.74e-01 4.76e+00 angle pdb=" C LEU A 583 " pdb=" N ASN A 584 " pdb=" CA ASN A 584 " ideal model delta sigma weight residual 121.54 125.29 -3.75 1.91e+00 2.74e-01 3.86e+00 angle pdb=" CA LEU A 462 " pdb=" CB LEU A 462 " pdb=" CG LEU A 462 " ideal model delta sigma weight residual 116.30 122.73 -6.43 3.50e+00 8.16e-02 3.38e+00 angle pdb=" CA GLU T 95 " pdb=" CB GLU T 95 " pdb=" CG GLU T 95 " ideal model delta sigma weight residual 114.10 117.69 -3.59 2.00e+00 2.50e-01 3.22e+00 ... (remaining 15411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.39: 6440 15.39 - 30.78: 296 30.78 - 46.17: 95 46.17 - 61.56: 23 61.56 - 76.95: 6 Dihedral angle restraints: 6860 sinusoidal: 2801 harmonic: 4059 Sorted by residual: dihedral pdb=" CA GLN A 633 " pdb=" C GLN A 633 " pdb=" N SER A 634 " pdb=" CA SER A 634 " ideal model delta harmonic sigma weight residual 180.00 163.49 16.51 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" N LEU B 12 " pdb=" CA LEU B 12 " pdb=" CB LEU B 12 " pdb=" CG LEU B 12 " ideal model delta sinusoidal sigma weight residual -60.00 -118.39 58.39 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N LEU C 12 " pdb=" CA LEU C 12 " pdb=" CB LEU C 12 " pdb=" CG LEU C 12 " ideal model delta sinusoidal sigma weight residual -60.00 -118.38 58.38 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 6857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1186 0.026 - 0.052: 363 0.052 - 0.079: 102 0.079 - 0.105: 87 0.105 - 0.131: 28 Chirality restraints: 1766 Sorted by residual: chirality pdb=" CA TRP T 49 " pdb=" N TRP T 49 " pdb=" C TRP T 49 " pdb=" CB TRP T 49 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA VAL A 515 " pdb=" N VAL A 515 " pdb=" C VAL A 515 " pdb=" CB VAL A 515 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 chirality pdb=" CA VAL B 167 " pdb=" N VAL B 167 " pdb=" C VAL B 167 " pdb=" CB VAL B 167 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 1763 not shown) Planarity restraints: 1977 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 120 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO A 121 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 335 " -0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO A 336 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 336 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 336 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 566 " 0.017 5.00e-02 4.00e+02 2.56e-02 1.04e+00 pdb=" N PRO A 567 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 567 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 567 " 0.013 5.00e-02 4.00e+02 ... (remaining 1974 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 195 2.65 - 3.21: 10572 3.21 - 3.77: 18966 3.77 - 4.34: 24018 4.34 - 4.90: 38948 Nonbonded interactions: 92699 Sorted by model distance: nonbonded pdb=" O2A ANP B 301 " pdb="MG MG B 302 " model vdw 2.082 2.170 nonbonded pdb=" N3B ANP C 301 " pdb="MG MG C 302 " model vdw 2.124 2.250 nonbonded pdb=" OG SER B 50 " pdb="MG MG B 302 " model vdw 2.162 2.170 nonbonded pdb=" N3B ANP B 301 " pdb="MG MG B 302 " model vdw 2.171 2.250 nonbonded pdb=" O LEU A 350 " pdb=" OH TYR A 382 " model vdw 2.173 3.040 ... (remaining 92694 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } 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 group one per residue 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: 1.300 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.340 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 : 0.002 0.047 11347 Z= 0.092 Angle : 0.458 6.434 15416 Z= 0.231 Chirality : 0.036 0.131 1766 Planarity : 0.003 0.027 1977 Dihedral : 10.674 76.950 4240 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.96 % Allowed : 6.04 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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 aren not related in a simple way. whole: 2.68 (0.23), residues: 1418 helix: 2.91 (0.19), residues: 748 sheet: 0.77 (0.36), residues: 196 loop : 0.40 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 608 TYR 0.008 0.001 TYR A 266 PHE 0.009 0.001 PHE T 165 TRP 0.008 0.001 TRP A 5 HIS 0.002 0.000 HIS C 89 Details of bonding type rmsd covalent geometry : bond 0.00177 (11347) covalent geometry : angle 0.45797 (15416) hydrogen bonds : bond 0.11383 ( 607) hydrogen bonds : angle 4.71224 ( 1761) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.9489 (tpp) cc_final: 0.9287 (mmm) REVERT: A 249 LEU cc_start: 0.9603 (tt) cc_final: 0.9248 (tt) REVERT: A 272 ASP cc_start: 0.9443 (OUTLIER) cc_final: 0.9137 (p0) REVERT: A 278 LYS cc_start: 0.9505 (tptp) cc_final: 0.9242 (tppt) REVERT: A 341 LEU cc_start: 0.9448 (mt) cc_final: 0.9017 (tt) REVERT: A 348 SER cc_start: 0.9501 (m) cc_final: 0.9261 (p) REVERT: A 557 ASP cc_start: 0.9357 (OUTLIER) cc_final: 0.8952 (p0) REVERT: A 575 MET cc_start: 0.9239 (ttt) cc_final: 0.8355 (tpp) REVERT: A 606 SER cc_start: 0.7723 (OUTLIER) cc_final: 0.7494 (m) REVERT: A 669 GLN cc_start: 0.9330 (mm110) cc_final: 0.9043 (mm110) REVERT: A 693 MET cc_start: 0.9511 (mmp) cc_final: 0.9225 (mmp) REVERT: A 711 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9126 (mm) REVERT: A 731 GLU cc_start: 0.9432 (tt0) cc_final: 0.9231 (pt0) REVERT: A 734 MET cc_start: 0.9314 (tmm) cc_final: 0.9053 (tmm) REVERT: A 735 LEU cc_start: 0.9571 (mt) cc_final: 0.9318 (mt) REVERT: B 12 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9177 (mm) REVERT: B 21 HIS cc_start: 0.9420 (t70) cc_final: 0.8988 (t70) REVERT: B 84 LYS cc_start: 0.9638 (tptp) cc_final: 0.9438 (tptp) REVERT: B 92 PHE cc_start: 0.8337 (t80) cc_final: 0.7967 (t80) REVERT: B 157 LEU cc_start: 0.9604 (mt) cc_final: 0.9116 (tp) REVERT: B 161 PHE cc_start: 0.9042 (m-10) cc_final: 0.8265 (m-80) REVERT: C 60 ASP cc_start: 0.8508 (t0) cc_final: 0.7798 (t0) REVERT: T 99 ASN cc_start: 0.9487 (OUTLIER) cc_final: 0.9126 (p0) REVERT: T 125 ASN cc_start: 0.9092 (m-40) cc_final: 0.8883 (m-40) REVERT: T 158 PHE cc_start: 0.7250 (m-80) cc_final: 0.6546 (m-80) outliers start: 23 outliers final: 4 residues processed: 229 average time/residue: 0.1194 time to fit residues: 38.1765 Evaluate side-chains 147 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 GLN A 501 GLN A 633 GLN A 701 GLN B 180 GLN C 125 ASN T 178 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.042956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.030370 restraints weight = 98097.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.031493 restraints weight = 66765.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.032328 restraints weight = 50421.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.032910 restraints weight = 40824.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.033371 restraints weight = 34919.303| |-----------------------------------------------------------------------------| r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11347 Z= 0.146 Angle : 0.602 7.913 15416 Z= 0.296 Chirality : 0.040 0.145 1766 Planarity : 0.003 0.029 1977 Dihedral : 5.175 59.536 1593 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.09 % Allowed : 2.47 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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 aren not related in a simple way. whole: 2.39 (0.23), residues: 1418 helix: 2.75 (0.19), residues: 750 sheet: 0.41 (0.34), residues: 201 loop : 0.21 (0.31), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 90 TYR 0.009 0.001 TYR T 143 PHE 0.016 0.001 PHE T 105 TRP 0.010 0.001 TRP A 641 HIS 0.006 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00306 (11347) covalent geometry : angle 0.60188 (15416) hydrogen bonds : bond 0.03845 ( 607) hydrogen bonds : angle 4.29073 ( 1761) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.9462 (tpp) cc_final: 0.9133 (mmm) REVERT: A 237 MET cc_start: 0.9664 (mtm) cc_final: 0.9385 (mtt) REVERT: A 249 LEU cc_start: 0.9635 (tt) cc_final: 0.8997 (tt) REVERT: A 341 LEU cc_start: 0.9500 (mt) cc_final: 0.9144 (tt) REVERT: A 575 MET cc_start: 0.9145 (ttt) cc_final: 0.8261 (tpp) REVERT: A 669 GLN cc_start: 0.9374 (mm110) cc_final: 0.9167 (mm110) REVERT: A 684 MET cc_start: 0.9423 (mmt) cc_final: 0.9015 (tpp) REVERT: A 693 MET cc_start: 0.9523 (mmp) cc_final: 0.9272 (mmp) REVERT: A 704 MET cc_start: 0.9388 (mmp) cc_final: 0.9185 (ttm) REVERT: A 711 LEU cc_start: 0.9560 (mm) cc_final: 0.9291 (mm) REVERT: A 731 GLU cc_start: 0.9394 (tt0) cc_final: 0.9188 (tt0) REVERT: A 734 MET cc_start: 0.9314 (tmm) cc_final: 0.9079 (tmm) REVERT: B 84 LYS cc_start: 0.9665 (tptp) cc_final: 0.9355 (tptp) REVERT: B 92 PHE cc_start: 0.8106 (t80) cc_final: 0.7820 (t80) REVERT: B 98 MET cc_start: 0.9085 (mpp) cc_final: 0.8514 (mtt) REVERT: B 157 LEU cc_start: 0.9627 (mt) cc_final: 0.9092 (tp) REVERT: B 161 PHE cc_start: 0.9116 (m-10) cc_final: 0.8305 (m-80) REVERT: B 162 ASN cc_start: 0.8694 (t0) cc_final: 0.8408 (t0) REVERT: C 60 ASP cc_start: 0.8834 (t0) cc_final: 0.8130 (t0) REVERT: C 162 ASN cc_start: 0.8793 (t0) cc_final: 0.8575 (t0) REVERT: T 141 ARG cc_start: 0.9545 (ptt90) cc_final: 0.9127 (mmt-90) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.1169 time to fit residues: 28.8982 Evaluate side-chains 130 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 19 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 94 optimal weight: 0.4980 chunk 55 optimal weight: 0.0980 chunk 42 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN C 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.043166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.030626 restraints weight = 96364.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.031742 restraints weight = 65705.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.032580 restraints weight = 49683.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.033181 restraints weight = 40238.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.033629 restraints weight = 34310.306| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11347 Z= 0.119 Angle : 0.546 6.425 15416 Z= 0.265 Chirality : 0.039 0.143 1766 Planarity : 0.003 0.038 1977 Dihedral : 5.260 58.619 1593 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.09 % Allowed : 3.06 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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 aren not related in a simple way. whole: 2.31 (0.23), residues: 1418 helix: 2.67 (0.19), residues: 751 sheet: 0.52 (0.35), residues: 196 loop : 0.13 (0.31), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 524 TYR 0.009 0.001 TYR T 171 PHE 0.013 0.001 PHE T 165 TRP 0.017 0.001 TRP A 5 HIS 0.004 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00252 (11347) covalent geometry : angle 0.54631 (15416) hydrogen bonds : bond 0.03695 ( 607) hydrogen bonds : angle 4.10557 ( 1761) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 LYS cc_start: 0.9599 (tptp) cc_final: 0.9397 (tppt) REVERT: A 341 LEU cc_start: 0.9498 (mt) cc_final: 0.9137 (tt) REVERT: A 402 MET cc_start: 0.8578 (mmp) cc_final: 0.8375 (pmm) REVERT: A 575 MET cc_start: 0.9175 (ttt) cc_final: 0.8326 (tpp) REVERT: A 669 GLN cc_start: 0.9324 (mm110) cc_final: 0.9120 (mm110) REVERT: A 684 MET cc_start: 0.9378 (mmt) cc_final: 0.9019 (tpp) REVERT: A 693 MET cc_start: 0.9515 (mmp) cc_final: 0.9279 (mmp) REVERT: A 711 LEU cc_start: 0.9545 (mm) cc_final: 0.9291 (mm) REVERT: A 731 GLU cc_start: 0.9367 (tt0) cc_final: 0.9154 (tt0) REVERT: A 734 MET cc_start: 0.9307 (tmm) cc_final: 0.9068 (tmm) REVERT: B 84 LYS cc_start: 0.9655 (tptp) cc_final: 0.9342 (tptp) REVERT: B 92 PHE cc_start: 0.8215 (t80) cc_final: 0.7865 (t80) REVERT: B 157 LEU cc_start: 0.9611 (mt) cc_final: 0.9046 (tp) REVERT: B 161 PHE cc_start: 0.9073 (m-10) cc_final: 0.8232 (m-80) REVERT: B 162 ASN cc_start: 0.8627 (t0) cc_final: 0.8361 (t0) REVERT: C 60 ASP cc_start: 0.8849 (t0) cc_final: 0.8092 (t0) REVERT: C 128 LYS cc_start: 0.9674 (tppt) cc_final: 0.9022 (tppp) REVERT: C 131 LEU cc_start: 0.9318 (mt) cc_final: 0.8928 (pp) REVERT: T 141 ARG cc_start: 0.9517 (ptt90) cc_final: 0.9252 (mmt-90) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.1120 time to fit residues: 26.1268 Evaluate side-chains 131 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 135 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 115 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 HIS C 125 ASN T 87 HIS ** T 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.041480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.029175 restraints weight = 99320.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.030250 restraints weight = 67471.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.031039 restraints weight = 51017.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.031599 restraints weight = 41474.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.031996 restraints weight = 35534.034| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11347 Z= 0.190 Angle : 0.616 9.324 15416 Z= 0.302 Chirality : 0.039 0.148 1766 Planarity : 0.003 0.028 1977 Dihedral : 5.370 59.650 1593 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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 aren not related in a simple way. whole: 2.10 (0.23), residues: 1418 helix: 2.48 (0.19), residues: 749 sheet: 0.45 (0.36), residues: 196 loop : 0.07 (0.31), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 524 TYR 0.013 0.002 TYR T 139 PHE 0.022 0.002 PHE T 105 TRP 0.014 0.001 TRP A 641 HIS 0.004 0.001 HIS C 11 Details of bonding type rmsd covalent geometry : bond 0.00390 (11347) covalent geometry : angle 0.61569 (15416) hydrogen bonds : bond 0.03796 ( 607) hydrogen bonds : angle 4.37325 ( 1761) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 LEU cc_start: 0.9521 (mt) cc_final: 0.9168 (tt) REVERT: A 402 MET cc_start: 0.8548 (mmp) cc_final: 0.8342 (pmm) REVERT: A 575 MET cc_start: 0.9224 (ttt) cc_final: 0.8457 (tpp) REVERT: A 684 MET cc_start: 0.9382 (mmt) cc_final: 0.9016 (tpp) REVERT: A 693 MET cc_start: 0.9515 (mmp) cc_final: 0.9278 (mmp) REVERT: A 708 HIS cc_start: 0.9084 (t70) cc_final: 0.8836 (t-90) REVERT: A 711 LEU cc_start: 0.9581 (mm) cc_final: 0.9287 (mm) REVERT: A 734 MET cc_start: 0.9301 (tmm) cc_final: 0.9020 (tmm) REVERT: A 735 LEU cc_start: 0.9574 (mt) cc_final: 0.8897 (mt) REVERT: B 84 LYS cc_start: 0.9657 (tptp) cc_final: 0.9353 (tptp) REVERT: B 92 PHE cc_start: 0.8172 (t80) cc_final: 0.7771 (t80) REVERT: B 162 ASN cc_start: 0.8737 (t0) cc_final: 0.8417 (t0) REVERT: B 202 MET cc_start: 0.9254 (ttm) cc_final: 0.8954 (tmm) REVERT: C 60 ASP cc_start: 0.8958 (t0) cc_final: 0.8176 (t0) REVERT: C 109 VAL cc_start: 0.9519 (m) cc_final: 0.9255 (p) REVERT: C 162 ASN cc_start: 0.8883 (t0) cc_final: 0.8664 (t0) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1156 time to fit residues: 25.6479 Evaluate side-chains 124 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 132 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 17 optimal weight: 0.0970 chunk 76 optimal weight: 30.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN T 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.042093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.029641 restraints weight = 96411.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.030709 restraints weight = 65482.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.031502 restraints weight = 49671.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.032074 restraints weight = 40392.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.032504 restraints weight = 34617.527| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11347 Z= 0.128 Angle : 0.572 7.461 15416 Z= 0.279 Chirality : 0.039 0.149 1766 Planarity : 0.003 0.028 1977 Dihedral : 5.398 64.787 1593 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.09 % Allowed : 1.87 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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 aren not related in a simple way. whole: 2.01 (0.23), residues: 1418 helix: 2.39 (0.19), residues: 752 sheet: 0.39 (0.36), residues: 200 loop : 0.06 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 524 TYR 0.010 0.001 TYR T 143 PHE 0.018 0.001 PHE T 158 TRP 0.017 0.001 TRP A 5 HIS 0.003 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00268 (11347) covalent geometry : angle 0.57196 (15416) hydrogen bonds : bond 0.03760 ( 607) hydrogen bonds : angle 4.30054 ( 1761) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 LEU cc_start: 0.9520 (mt) cc_final: 0.9181 (tt) REVERT: A 402 MET cc_start: 0.8531 (mmp) cc_final: 0.8307 (pmm) REVERT: A 575 MET cc_start: 0.9230 (ttt) cc_final: 0.8432 (tpp) REVERT: A 693 MET cc_start: 0.9509 (mmp) cc_final: 0.9274 (mmp) REVERT: A 704 MET cc_start: 0.9451 (mmm) cc_final: 0.9152 (mmm) REVERT: A 708 HIS cc_start: 0.9063 (t70) cc_final: 0.8760 (t-90) REVERT: A 711 LEU cc_start: 0.9572 (mm) cc_final: 0.9339 (mm) REVERT: A 735 LEU cc_start: 0.9571 (mt) cc_final: 0.9339 (mt) REVERT: B 84 LYS cc_start: 0.9656 (tptp) cc_final: 0.9347 (tptp) REVERT: B 92 PHE cc_start: 0.8156 (t80) cc_final: 0.7717 (t80) REVERT: B 162 ASN cc_start: 0.8702 (t0) cc_final: 0.8416 (t0) REVERT: B 202 MET cc_start: 0.9438 (ttp) cc_final: 0.8783 (tmm) REVERT: C 60 ASP cc_start: 0.8982 (t0) cc_final: 0.8221 (t0) REVERT: C 77 MET cc_start: 0.8507 (mtm) cc_final: 0.8299 (mtt) REVERT: C 109 VAL cc_start: 0.9516 (m) cc_final: 0.9258 (p) REVERT: C 162 ASN cc_start: 0.8822 (t0) cc_final: 0.8608 (t0) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.1126 time to fit residues: 25.0266 Evaluate side-chains 118 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 86 optimal weight: 20.0000 chunk 42 optimal weight: 9.9990 chunk 116 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 37 optimal weight: 0.1980 chunk 73 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 overall best weight: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.041058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.029014 restraints weight = 99487.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.030091 restraints weight = 67000.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.030902 restraints weight = 50225.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.031459 restraints weight = 40564.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.031831 restraints weight = 34721.951| |-----------------------------------------------------------------------------| r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11347 Z= 0.194 Angle : 0.625 8.343 15416 Z= 0.309 Chirality : 0.039 0.151 1766 Planarity : 0.004 0.028 1977 Dihedral : 5.542 66.598 1593 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.17 % Allowed : 1.96 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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 aren not related in a simple way. whole: 1.75 (0.23), residues: 1418 helix: 2.17 (0.19), residues: 751 sheet: 0.30 (0.38), residues: 185 loop : -0.04 (0.31), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 474 TYR 0.017 0.002 TYR T 171 PHE 0.036 0.002 PHE T 158 TRP 0.067 0.002 TRP A 481 HIS 0.003 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00393 (11347) covalent geometry : angle 0.62525 (15416) hydrogen bonds : bond 0.03812 ( 607) hydrogen bonds : angle 4.45564 ( 1761) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 MET cc_start: 0.8649 (ppp) cc_final: 0.8446 (ppp) REVERT: A 175 MET cc_start: 0.9483 (mmm) cc_final: 0.9175 (tpp) REVERT: A 341 LEU cc_start: 0.9530 (mt) cc_final: 0.9198 (tt) REVERT: A 402 MET cc_start: 0.8536 (mmp) cc_final: 0.8303 (pmm) REVERT: A 575 MET cc_start: 0.9275 (ttt) cc_final: 0.8538 (tpp) REVERT: A 684 MET cc_start: 0.9423 (mmt) cc_final: 0.9124 (tpp) REVERT: A 693 MET cc_start: 0.9511 (mmp) cc_final: 0.9277 (mmp) REVERT: A 704 MET cc_start: 0.9437 (mmm) cc_final: 0.9149 (mmm) REVERT: A 708 HIS cc_start: 0.9172 (t70) cc_final: 0.8742 (t-90) REVERT: A 711 LEU cc_start: 0.9594 (mm) cc_final: 0.9349 (mm) REVERT: A 735 LEU cc_start: 0.9672 (mt) cc_final: 0.9465 (mt) REVERT: B 84 LYS cc_start: 0.9655 (tptp) cc_final: 0.9354 (tptp) REVERT: B 92 PHE cc_start: 0.8229 (t80) cc_final: 0.7768 (t80) REVERT: B 162 ASN cc_start: 0.8743 (t0) cc_final: 0.8470 (t0) REVERT: B 202 MET cc_start: 0.9441 (ttp) cc_final: 0.8738 (tmm) REVERT: C 60 ASP cc_start: 0.9033 (t0) cc_final: 0.8262 (t0) REVERT: C 109 VAL cc_start: 0.9531 (m) cc_final: 0.9267 (p) REVERT: T 157 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7212 (pm20) outliers start: 2 outliers final: 0 residues processed: 147 average time/residue: 0.1049 time to fit residues: 22.1499 Evaluate side-chains 115 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 12 optimal weight: 0.0980 chunk 10 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.042248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.029968 restraints weight = 94161.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.031093 restraints weight = 63367.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.031883 restraints weight = 47653.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.032436 restraints weight = 38591.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.032874 restraints weight = 33103.229| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11347 Z= 0.111 Angle : 0.583 8.572 15416 Z= 0.282 Chirality : 0.040 0.148 1766 Planarity : 0.003 0.028 1977 Dihedral : 5.507 69.469 1593 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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 aren not related in a simple way. whole: 1.98 (0.23), residues: 1418 helix: 2.40 (0.19), residues: 745 sheet: 0.36 (0.36), residues: 200 loop : 0.04 (0.31), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG T 141 TYR 0.016 0.001 TYR T 139 PHE 0.018 0.001 PHE A 732 TRP 0.041 0.001 TRP A 481 HIS 0.003 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00235 (11347) covalent geometry : angle 0.58250 (15416) hydrogen bonds : bond 0.03744 ( 607) hydrogen bonds : angle 4.22767 ( 1761) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.9246 (tpt) cc_final: 0.8551 (tpp) REVERT: A 170 MET cc_start: 0.8473 (ppp) cc_final: 0.8252 (ppp) REVERT: A 175 MET cc_start: 0.9421 (mmm) cc_final: 0.9151 (tpp) REVERT: A 341 LEU cc_start: 0.9512 (mt) cc_final: 0.9123 (tt) REVERT: A 402 MET cc_start: 0.8471 (mmp) cc_final: 0.8266 (pmm) REVERT: A 575 MET cc_start: 0.9241 (ttt) cc_final: 0.8475 (tpp) REVERT: A 693 MET cc_start: 0.9516 (mmp) cc_final: 0.9278 (mmp) REVERT: A 704 MET cc_start: 0.9456 (mmm) cc_final: 0.9178 (mmm) REVERT: A 708 HIS cc_start: 0.9036 (t70) cc_final: 0.8663 (t-90) REVERT: A 711 LEU cc_start: 0.9574 (mm) cc_final: 0.9300 (mm) REVERT: B 84 LYS cc_start: 0.9649 (tptp) cc_final: 0.9330 (tptp) REVERT: B 92 PHE cc_start: 0.8197 (t80) cc_final: 0.7703 (t80) REVERT: B 162 ASN cc_start: 0.8668 (t0) cc_final: 0.8412 (t0) REVERT: B 202 MET cc_start: 0.9431 (ttp) cc_final: 0.8774 (tmm) REVERT: C 60 ASP cc_start: 0.9035 (t0) cc_final: 0.8287 (t0) REVERT: C 77 MET cc_start: 0.8643 (mtm) cc_final: 0.8429 (mtt) REVERT: C 109 VAL cc_start: 0.9514 (m) cc_final: 0.9264 (p) REVERT: C 131 LEU cc_start: 0.9381 (mt) cc_final: 0.9071 (pp) REVERT: C 162 ASN cc_start: 0.8915 (t0) cc_final: 0.8699 (t0) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.0983 time to fit residues: 22.5444 Evaluate side-chains 118 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 20.0000 chunk 133 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 85 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 18 optimal weight: 40.0000 chunk 27 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.041392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.029176 restraints weight = 96761.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.030239 restraints weight = 65397.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.031024 restraints weight = 49456.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.031565 restraints weight = 40229.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.031972 restraints weight = 34662.170| |-----------------------------------------------------------------------------| r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11347 Z= 0.151 Angle : 0.603 9.847 15416 Z= 0.296 Chirality : 0.039 0.151 1766 Planarity : 0.003 0.035 1977 Dihedral : 5.481 68.125 1593 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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 aren not related in a simple way. whole: 1.87 (0.23), residues: 1418 helix: 2.32 (0.19), residues: 744 sheet: 0.28 (0.36), residues: 201 loop : -0.04 (0.31), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 90 TYR 0.007 0.001 TYR T 139 PHE 0.023 0.002 PHE A 732 TRP 0.029 0.002 TRP A 481 HIS 0.003 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00314 (11347) covalent geometry : angle 0.60301 (15416) hydrogen bonds : bond 0.03710 ( 607) hydrogen bonds : angle 4.39333 ( 1761) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.9337 (tpt) cc_final: 0.8490 (tpp) REVERT: A 170 MET cc_start: 0.8512 (ppp) cc_final: 0.8289 (ppp) REVERT: A 175 MET cc_start: 0.9406 (mmm) cc_final: 0.9118 (tpp) REVERT: A 263 MET cc_start: 0.9094 (ppp) cc_final: 0.8828 (ppp) REVERT: A 341 LEU cc_start: 0.9532 (mt) cc_final: 0.9184 (tt) REVERT: A 402 MET cc_start: 0.8535 (mmp) cc_final: 0.8301 (pmm) REVERT: A 417 LEU cc_start: 0.9625 (mt) cc_final: 0.9419 (pp) REVERT: A 575 MET cc_start: 0.9266 (ttt) cc_final: 0.8523 (tpp) REVERT: A 693 MET cc_start: 0.9512 (mmp) cc_final: 0.9278 (mmp) REVERT: A 704 MET cc_start: 0.9446 (mmm) cc_final: 0.9165 (mmm) REVERT: A 708 HIS cc_start: 0.9134 (t70) cc_final: 0.8695 (t-90) REVERT: A 735 LEU cc_start: 0.9670 (mt) cc_final: 0.9449 (mt) REVERT: B 84 LYS cc_start: 0.9669 (tptp) cc_final: 0.9368 (tptp) REVERT: B 92 PHE cc_start: 0.8294 (t80) cc_final: 0.7799 (t80) REVERT: B 162 ASN cc_start: 0.8674 (t0) cc_final: 0.8429 (t0) REVERT: B 202 MET cc_start: 0.9425 (ttp) cc_final: 0.8856 (tmm) REVERT: C 60 ASP cc_start: 0.9089 (t0) cc_final: 0.8374 (t0) REVERT: C 77 MET cc_start: 0.8672 (mtm) cc_final: 0.8331 (ptp) REVERT: C 109 VAL cc_start: 0.9540 (m) cc_final: 0.9306 (p) REVERT: C 162 ASN cc_start: 0.8942 (t0) cc_final: 0.8718 (t0) REVERT: T 131 MET cc_start: 0.7640 (tpt) cc_final: 0.7362 (tpt) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1057 time to fit residues: 22.6679 Evaluate side-chains 115 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 3 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 65 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 HIS ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.040352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.028307 restraints weight = 99824.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.029342 restraints weight = 67117.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.030098 restraints weight = 50447.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.030630 restraints weight = 41218.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.031013 restraints weight = 35532.733| |-----------------------------------------------------------------------------| r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11347 Z= 0.220 Angle : 0.679 9.079 15416 Z= 0.336 Chirality : 0.040 0.149 1766 Planarity : 0.004 0.047 1977 Dihedral : 5.799 71.791 1593 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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 aren not related in a simple way. whole: 1.37 (0.23), residues: 1418 helix: 1.86 (0.19), residues: 762 sheet: 0.09 (0.37), residues: 191 loop : -0.26 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 131 TYR 0.010 0.001 TYR T 171 PHE 0.027 0.002 PHE A 732 TRP 0.021 0.002 TRP A 5 HIS 0.003 0.001 HIS C 10 Details of bonding type rmsd covalent geometry : bond 0.00445 (11347) covalent geometry : angle 0.67886 (15416) hydrogen bonds : bond 0.04111 ( 607) hydrogen bonds : angle 4.70102 ( 1761) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.9395 (tpt) cc_final: 0.8581 (tpp) REVERT: A 133 MET cc_start: 0.9210 (mmp) cc_final: 0.8957 (mmp) REVERT: A 175 MET cc_start: 0.9289 (mmm) cc_final: 0.9064 (tpp) REVERT: A 341 LEU cc_start: 0.9560 (mt) cc_final: 0.9216 (tt) REVERT: A 402 MET cc_start: 0.8490 (mmp) cc_final: 0.8273 (pmm) REVERT: A 575 MET cc_start: 0.9273 (ttt) cc_final: 0.8607 (tpp) REVERT: A 693 MET cc_start: 0.9511 (mmp) cc_final: 0.9265 (mmp) REVERT: A 704 MET cc_start: 0.9411 (mmm) cc_final: 0.9148 (mmm) REVERT: A 735 LEU cc_start: 0.9668 (mt) cc_final: 0.9426 (mt) REVERT: B 92 PHE cc_start: 0.8466 (t80) cc_final: 0.8019 (t80) REVERT: B 162 ASN cc_start: 0.8715 (t0) cc_final: 0.8442 (t0) REVERT: B 202 MET cc_start: 0.9433 (ttp) cc_final: 0.8803 (tmm) REVERT: C 60 ASP cc_start: 0.9092 (t0) cc_final: 0.8287 (t0) REVERT: C 61 ASP cc_start: 0.8667 (m-30) cc_final: 0.8294 (p0) REVERT: C 109 VAL cc_start: 0.9614 (m) cc_final: 0.9366 (p) REVERT: C 115 LEU cc_start: 0.9175 (mp) cc_final: 0.8953 (mp) REVERT: C 162 ASN cc_start: 0.8910 (t0) cc_final: 0.8703 (t0) REVERT: T 131 MET cc_start: 0.7734 (tpt) cc_final: 0.7514 (tpt) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1023 time to fit residues: 21.8514 Evaluate side-chains 107 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 49 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 91 optimal weight: 0.0770 chunk 128 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.041515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.029134 restraints weight = 97514.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.030231 restraints weight = 65578.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.031035 restraints weight = 49289.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.031444 restraints weight = 39943.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.031952 restraints weight = 34949.156| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11347 Z= 0.123 Angle : 0.605 9.923 15416 Z= 0.294 Chirality : 0.040 0.155 1766 Planarity : 0.003 0.028 1977 Dihedral : 5.700 71.990 1593 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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 aren not related in a simple way. whole: 1.54 (0.23), residues: 1418 helix: 2.01 (0.19), residues: 763 sheet: 0.23 (0.37), residues: 186 loop : -0.24 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 239 TYR 0.012 0.001 TYR T 139 PHE 0.022 0.002 PHE B 97 TRP 0.033 0.002 TRP A 5 HIS 0.004 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00259 (11347) covalent geometry : angle 0.60454 (15416) hydrogen bonds : bond 0.03861 ( 607) hydrogen bonds : angle 4.35568 ( 1761) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.9699 (mm) cc_final: 0.9421 (tp) REVERT: A 51 MET cc_start: 0.9318 (tpt) cc_final: 0.8862 (tpp) REVERT: A 175 MET cc_start: 0.9256 (mmm) cc_final: 0.8894 (tpp) REVERT: A 198 LYS cc_start: 0.9344 (mmtt) cc_final: 0.9094 (pptt) REVERT: A 238 GLU cc_start: 0.9645 (pt0) cc_final: 0.9421 (pp20) REVERT: A 341 LEU cc_start: 0.9534 (mt) cc_final: 0.9213 (tt) REVERT: A 402 MET cc_start: 0.8508 (mmp) cc_final: 0.8251 (pmm) REVERT: A 417 LEU cc_start: 0.9629 (mt) cc_final: 0.9417 (pp) REVERT: A 481 TRP cc_start: 0.8951 (m-90) cc_final: 0.8556 (m-90) REVERT: A 575 MET cc_start: 0.9238 (ttt) cc_final: 0.8559 (tpp) REVERT: A 693 MET cc_start: 0.9526 (mmp) cc_final: 0.9296 (mmp) REVERT: A 704 MET cc_start: 0.9446 (mmm) cc_final: 0.9201 (mmp) REVERT: A 735 LEU cc_start: 0.9659 (mt) cc_final: 0.9422 (mt) REVERT: B 92 PHE cc_start: 0.8404 (t80) cc_final: 0.7922 (t80) REVERT: B 162 ASN cc_start: 0.8617 (t0) cc_final: 0.8344 (t0) REVERT: B 202 MET cc_start: 0.9432 (ttp) cc_final: 0.8838 (tmm) REVERT: C 60 ASP cc_start: 0.9115 (t0) cc_final: 0.8305 (t0) REVERT: C 61 ASP cc_start: 0.8608 (m-30) cc_final: 0.8261 (p0) REVERT: C 77 MET cc_start: 0.8729 (mtm) cc_final: 0.8406 (ptp) REVERT: C 109 VAL cc_start: 0.9581 (m) cc_final: 0.9375 (p) REVERT: C 115 LEU cc_start: 0.9188 (mp) cc_final: 0.8971 (mp) REVERT: C 162 ASN cc_start: 0.8912 (t0) cc_final: 0.8699 (t0) REVERT: C 202 MET cc_start: 0.8535 (tmm) cc_final: 0.8271 (tmm) REVERT: T 131 MET cc_start: 0.7620 (tpt) cc_final: 0.7358 (tpt) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1041 time to fit residues: 23.0055 Evaluate side-chains 116 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 106 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 131 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 456 GLN ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.040499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.028386 restraints weight = 98601.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.029435 restraints weight = 66396.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.030173 restraints weight = 50101.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.030739 restraints weight = 40900.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.031128 restraints weight = 35089.098| |-----------------------------------------------------------------------------| r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11347 Z= 0.186 Angle : 0.644 8.680 15416 Z= 0.318 Chirality : 0.040 0.150 1766 Planarity : 0.004 0.031 1977 Dihedral : 5.745 71.368 1593 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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 aren not related in a simple way. whole: 1.48 (0.23), residues: 1418 helix: 1.96 (0.19), residues: 759 sheet: 0.21 (0.37), residues: 192 loop : -0.25 (0.31), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 90 TYR 0.008 0.001 TYR A 266 PHE 0.029 0.002 PHE A 732 TRP 0.024 0.002 TRP A 5 HIS 0.005 0.001 HIS A 708 Details of bonding type rmsd covalent geometry : bond 0.00380 (11347) covalent geometry : angle 0.64414 (15416) hydrogen bonds : bond 0.03948 ( 607) hydrogen bonds : angle 4.56592 ( 1761) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1907.47 seconds wall clock time: 33 minutes 46.77 seconds (2026.77 seconds total)