Starting phenix.real_space_refine on Mon Jun 9 23:27:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ge8_51293/06_2025/9ge8_51293.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ge8_51293/06_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_51293/06_2025/9ge8_51293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ge8_51293/06_2025/9ge8_51293.map" model { file = "/net/cci-nas-00/data/ceres_data/9ge8_51293/06_2025/9ge8_51293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ge8_51293/06_2025/9ge8_51293.cif" } resolution = 4.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.29, per 1000 atoms: 0.57 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: 2.70 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.02 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: 3.19 Time building geometry restraints manager: 3.18 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: 0.710 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.690 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.860 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP A 5 HIS 0.002 0.000 HIS C 89 PHE 0.009 0.001 PHE T 165 TYR 0.008 0.001 TYR A 266 ARG 0.002 0.000 ARG A 608 Details of bonding type rmsd hydrogen bonds : bond 0.11383 ( 607) hydrogen bonds : angle 4.71224 ( 1761) covalent geometry : bond 0.00177 (11347) covalent geometry : angle 0.45797 (15416) *********************** 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 : 1.163 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: 0.2426 time to fit residues: 76.9207 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 : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 72 optimal weight: 0.0870 chunk 57 optimal weight: 50.0000 chunk 110 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 67 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 overall best weight: 2.3562 ------------------------------------------------------------------------------- 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 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3140 r_free = 0.3140 target = 0.043230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.030684 restraints weight = 95594.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.031771 restraints weight = 65417.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.032583 restraints weight = 49802.393| |-----------------------------------------------------------------------------| r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1606 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= 0.135 Angle : 0.585 7.583 15416 Z= 0.287 Chirality : 0.040 0.149 1766 Planarity : 0.003 0.029 1977 Dihedral : 5.154 59.629 1593 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.23), residues: 1418 helix: 2.79 (0.19), residues: 750 sheet: 0.55 (0.35), residues: 196 loop : 0.21 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP T 176 HIS 0.005 0.001 HIS B 89 PHE 0.014 0.001 PHE T 105 TYR 0.009 0.001 TYR A 266 ARG 0.005 0.000 ARG T 90 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 607) hydrogen bonds : angle 4.21860 ( 1761) covalent geometry : bond 0.00282 (11347) covalent geometry : angle 0.58515 (15416) *********************** 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 180 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 1.366 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: 0.9460 (tpp) cc_final: 0.9146 (mmm) REVERT: A 237 MET cc_start: 0.9670 (mtm) cc_final: 0.9376 (mtt) REVERT: A 249 LEU cc_start: 0.9629 (tt) cc_final: 0.8994 (tt) REVERT: A 278 LYS cc_start: 0.9610 (tptp) cc_final: 0.9398 (tppt) REVERT: A 341 LEU cc_start: 0.9487 (mt) cc_final: 0.9151 (tt) REVERT: A 575 MET cc_start: 0.9155 (ttt) cc_final: 0.8256 (tpp) REVERT: A 669 GLN cc_start: 0.9367 (mm110) cc_final: 0.9167 (mm110) REVERT: A 684 MET cc_start: 0.9422 (mmt) cc_final: 0.8991 (tpp) REVERT: A 693 MET cc_start: 0.9550 (mmp) cc_final: 0.9280 (mmp) REVERT: A 704 MET cc_start: 0.9373 (mmp) cc_final: 0.9165 (ttm) REVERT: A 711 LEU cc_start: 0.9539 (mm) cc_final: 0.9271 (mm) REVERT: A 734 MET cc_start: 0.9325 (tmm) cc_final: 0.9081 (tmm) REVERT: B 84 LYS cc_start: 0.9659 (tptp) cc_final: 0.9340 (tptp) REVERT: B 92 PHE cc_start: 0.8091 (t80) cc_final: 0.7786 (t80) REVERT: B 98 MET cc_start: 0.9062 (mpp) cc_final: 0.8521 (mtt) REVERT: B 157 LEU cc_start: 0.9638 (mt) cc_final: 0.9102 (tp) REVERT: B 161 PHE cc_start: 0.9125 (m-10) cc_final: 0.8316 (m-80) REVERT: B 162 ASN cc_start: 0.8636 (t0) cc_final: 0.8380 (t0) REVERT: C 60 ASP cc_start: 0.8883 (t0) cc_final: 0.8187 (t0) REVERT: C 88 LYS cc_start: 0.9675 (mmmm) cc_final: 0.9383 (mmmm) REVERT: T 141 ARG cc_start: 0.9550 (ptt90) cc_final: 0.9137 (mmt-90) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.2644 time to fit residues: 65.7291 Evaluate side-chains 135 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 120 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 14 optimal weight: 30.0000 chunk 87 optimal weight: 0.4980 chunk 118 optimal weight: 0.0030 chunk 138 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.043597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.031061 restraints weight = 95107.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.032196 restraints weight = 64590.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.033018 restraints weight = 48743.020| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1944 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= 0.109 Angle : 0.538 7.605 15416 Z= 0.260 Chirality : 0.039 0.141 1766 Planarity : 0.003 0.030 1977 Dihedral : 5.202 59.058 1593 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.09 % Allowed : 2.38 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.23), residues: 1418 helix: 2.68 (0.19), residues: 751 sheet: 0.58 (0.35), residues: 196 loop : 0.15 (0.31), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 5 HIS 0.005 0.001 HIS B 89 PHE 0.011 0.001 PHE A 165 TYR 0.009 0.001 TYR T 171 ARG 0.003 0.000 ARG T 90 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 607) hydrogen bonds : angle 4.04928 ( 1761) covalent geometry : bond 0.00229 (11347) covalent geometry : angle 0.53766 (15416) *********************** 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 173 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 1.281 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: A 278 LYS cc_start: 0.9635 (tptp) cc_final: 0.9399 (tppt) REVERT: A 341 LEU cc_start: 0.9496 (mt) cc_final: 0.9121 (tt) REVERT: A 402 MET cc_start: 0.8584 (mmp) cc_final: 0.8364 (pmm) REVERT: A 417 LEU cc_start: 0.9562 (mt) cc_final: 0.9265 (tp) REVERT: A 575 MET cc_start: 0.9167 (ttt) cc_final: 0.8294 (tpp) REVERT: A 669 GLN cc_start: 0.9349 (mm110) cc_final: 0.9135 (mm110) REVERT: A 684 MET cc_start: 0.9375 (mmt) cc_final: 0.9014 (tpp) REVERT: A 693 MET cc_start: 0.9549 (mmp) cc_final: 0.9287 (mmp) REVERT: A 711 LEU cc_start: 0.9541 (mm) cc_final: 0.9278 (mm) REVERT: A 734 MET cc_start: 0.9307 (tmm) cc_final: 0.9082 (tmm) REVERT: B 84 LYS cc_start: 0.9651 (tptp) cc_final: 0.9327 (tptp) REVERT: B 92 PHE cc_start: 0.8156 (t80) cc_final: 0.7781 (t80) REVERT: B 98 MET cc_start: 0.9117 (mpp) cc_final: 0.8483 (mtt) REVERT: B 157 LEU cc_start: 0.9625 (mt) cc_final: 0.9073 (tp) REVERT: B 161 PHE cc_start: 0.9086 (m-10) cc_final: 0.8264 (m-80) REVERT: B 162 ASN cc_start: 0.8637 (t0) cc_final: 0.8375 (t0) REVERT: C 128 LYS cc_start: 0.9679 (tppt) cc_final: 0.9117 (tppt) REVERT: C 131 LEU cc_start: 0.9326 (mt) cc_final: 0.9005 (pp) REVERT: C 162 ASN cc_start: 0.8805 (t0) cc_final: 0.8593 (t0) REVERT: T 141 ARG cc_start: 0.9550 (ptt90) cc_final: 0.9275 (mmt-90) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.2459 time to fit residues: 59.8594 Evaluate side-chains 139 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 77 optimal weight: 9.9990 chunk 54 optimal weight: 30.0000 chunk 10 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 T 87 HIS ** T 109 GLN ** 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 = 0.3062 r_free = 0.3062 target = 0.040954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.028774 restraints weight = 100199.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.029843 restraints weight = 68577.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.030615 restraints weight = 51617.755| |-----------------------------------------------------------------------------| r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11347 Z= 0.242 Angle : 0.697 9.918 15416 Z= 0.342 Chirality : 0.041 0.151 1766 Planarity : 0.004 0.038 1977 Dihedral : 5.526 60.511 1593 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.23), residues: 1418 helix: 2.28 (0.19), residues: 749 sheet: 0.33 (0.36), residues: 189 loop : 0.13 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 641 HIS 0.005 0.002 HIS C 89 PHE 0.025 0.002 PHE T 105 TYR 0.012 0.002 TYR T 143 ARG 0.005 0.001 ARG A 524 Details of bonding type rmsd hydrogen bonds : bond 0.04068 ( 607) hydrogen bonds : angle 4.61640 ( 1761) covalent geometry : bond 0.00485 (11347) covalent geometry : angle 0.69737 (15416) *********************** 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 : 1.248 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: A 341 LEU cc_start: 0.9547 (mt) cc_final: 0.9213 (tt) REVERT: A 344 MET cc_start: 0.9514 (tmm) cc_final: 0.9312 (tmm) REVERT: A 402 MET cc_start: 0.8571 (mmp) cc_final: 0.8363 (pmm) REVERT: A 417 LEU cc_start: 0.9621 (mt) cc_final: 0.9327 (tp) REVERT: A 575 MET cc_start: 0.9264 (ttt) cc_final: 0.8526 (tpp) REVERT: A 684 MET cc_start: 0.9397 (mmt) cc_final: 0.9005 (tpp) REVERT: A 693 MET cc_start: 0.9540 (mmp) cc_final: 0.9293 (mmp) REVERT: A 708 HIS cc_start: 0.9209 (t70) cc_final: 0.8815 (t-90) REVERT: A 711 LEU cc_start: 0.9599 (mm) cc_final: 0.9334 (mm) REVERT: A 731 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8631 (mm-30) REVERT: A 734 MET cc_start: 0.9337 (tmm) cc_final: 0.9101 (tmm) REVERT: B 84 LYS cc_start: 0.9667 (tptp) cc_final: 0.9380 (tptp) REVERT: B 92 PHE cc_start: 0.8231 (t80) cc_final: 0.7697 (t80) REVERT: B 162 ASN cc_start: 0.8808 (t0) cc_final: 0.8514 (t0) REVERT: C 141 ASP cc_start: 0.9231 (p0) cc_final: 0.9025 (p0) REVERT: C 165 PRO cc_start: 0.7957 (Cg_endo) cc_final: 0.7739 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.2281 time to fit residues: 51.7493 Evaluate side-chains 120 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 116 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 139 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- 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** ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 109 GLN ** 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 = 0.3089 r_free = 0.3089 target = 0.041716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.029325 restraints weight = 97226.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.030417 restraints weight = 66330.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031222 restraints weight = 49930.535| |-----------------------------------------------------------------------------| r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11347 Z= 0.135 Angle : 0.586 7.954 15416 Z= 0.287 Chirality : 0.039 0.148 1766 Planarity : 0.003 0.040 1977 Dihedral : 5.511 65.658 1593 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.23), residues: 1418 helix: 2.36 (0.19), residues: 750 sheet: 0.35 (0.37), residues: 189 loop : 0.09 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 641 HIS 0.004 0.001 HIS B 89 PHE 0.024 0.002 PHE B 97 TYR 0.010 0.001 TYR T 143 ARG 0.006 0.000 ARG A 524 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 607) hydrogen bonds : angle 4.38775 ( 1761) covalent geometry : bond 0.00284 (11347) covalent geometry : angle 0.58629 (15416) *********************** 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 154 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.392 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: A 133 MET cc_start: 0.9031 (mmp) cc_final: 0.8798 (mmm) REVERT: A 341 LEU cc_start: 0.9534 (mt) cc_final: 0.9180 (tt) REVERT: A 402 MET cc_start: 0.8552 (mmp) cc_final: 0.8307 (pmm) REVERT: A 481 TRP cc_start: 0.9069 (m-10) cc_final: 0.8846 (m-90) REVERT: A 575 MET cc_start: 0.9244 (ttt) cc_final: 0.8506 (tpp) REVERT: A 693 MET cc_start: 0.9536 (mmp) cc_final: 0.9293 (mmp) REVERT: A 704 MET cc_start: 0.9458 (mmm) cc_final: 0.9172 (mmm) REVERT: A 708 HIS cc_start: 0.9184 (t70) cc_final: 0.8788 (t-90) REVERT: A 711 LEU cc_start: 0.9571 (mm) cc_final: 0.9344 (mm) REVERT: A 735 LEU cc_start: 0.9610 (mt) cc_final: 0.9408 (mt) REVERT: B 84 LYS cc_start: 0.9659 (tptp) cc_final: 0.9350 (tptp) REVERT: B 92 PHE cc_start: 0.8181 (t80) cc_final: 0.7774 (t80) REVERT: B 162 ASN cc_start: 0.8742 (t0) cc_final: 0.8476 (t0) REVERT: C 141 ASP cc_start: 0.9201 (p0) cc_final: 0.8977 (p0) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2444 time to fit residues: 54.8408 Evaluate side-chains 120 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 41 optimal weight: 0.6980 chunk 136 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 131 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 94 optimal weight: 0.4980 overall best weight: 2.8184 ------------------------------------------------------------------------------- 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** C 125 ASN ** 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 = 0.3085 r_free = 0.3085 target = 0.041601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.029220 restraints weight = 96632.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.030326 restraints weight = 65363.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031128 restraints weight = 49308.911| |-----------------------------------------------------------------------------| r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2795 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= 0.129 Angle : 0.569 7.679 15416 Z= 0.279 Chirality : 0.039 0.149 1766 Planarity : 0.003 0.028 1977 Dihedral : 5.492 66.638 1593 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.23), residues: 1418 helix: 2.34 (0.19), residues: 751 sheet: 0.35 (0.36), residues: 198 loop : 0.08 (0.31), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 641 HIS 0.003 0.001 HIS B 89 PHE 0.033 0.002 PHE T 158 TYR 0.011 0.001 TYR T 171 ARG 0.004 0.000 ARG T 141 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 607) hydrogen bonds : angle 4.26665 ( 1761) covalent geometry : bond 0.00272 (11347) covalent geometry : angle 0.56895 (15416) *********************** 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 156 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 1.340 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: A 175 MET cc_start: 0.9448 (tpt) cc_final: 0.9185 (tpp) REVERT: A 341 LEU cc_start: 0.9529 (mt) cc_final: 0.9181 (tt) REVERT: A 402 MET cc_start: 0.8567 (mmp) cc_final: 0.8328 (pmm) REVERT: A 575 MET cc_start: 0.9260 (ttt) cc_final: 0.8520 (tpp) REVERT: A 693 MET cc_start: 0.9538 (mmp) cc_final: 0.9304 (mmp) REVERT: A 708 HIS cc_start: 0.9142 (t70) cc_final: 0.8730 (t-90) REVERT: A 711 LEU cc_start: 0.9588 (mm) cc_final: 0.9319 (mm) REVERT: A 731 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8564 (mm-30) REVERT: A 735 LEU cc_start: 0.9623 (mt) cc_final: 0.9413 (mt) REVERT: B 84 LYS cc_start: 0.9666 (tptp) cc_final: 0.9353 (tptp) REVERT: B 92 PHE cc_start: 0.8209 (t80) cc_final: 0.7745 (t80) REVERT: B 162 ASN cc_start: 0.8751 (t0) cc_final: 0.8492 (t0) REVERT: B 202 MET cc_start: 0.9278 (ttm) cc_final: 0.9022 (tmm) REVERT: C 60 ASP cc_start: 0.8783 (m-30) cc_final: 0.8283 (t70) REVERT: C 61 ASP cc_start: 0.8855 (p0) cc_final: 0.8455 (p0) REVERT: C 141 ASP cc_start: 0.9201 (p0) cc_final: 0.9000 (p0) outliers start: 2 outliers final: 0 residues processed: 156 average time/residue: 0.2153 time to fit residues: 49.1935 Evaluate side-chains 117 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 115 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 14 optimal weight: 50.0000 chunk 140 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- 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 T 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.041725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.029376 restraints weight = 96862.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.030463 restraints weight = 65604.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.031276 restraints weight = 49537.399| |-----------------------------------------------------------------------------| r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2920 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= 0.125 Angle : 0.579 9.597 15416 Z= 0.280 Chirality : 0.039 0.149 1766 Planarity : 0.003 0.028 1977 Dihedral : 5.468 68.042 1593 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.09 % Allowed : 0.94 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.23), residues: 1418 helix: 2.35 (0.19), residues: 750 sheet: 0.35 (0.36), residues: 198 loop : 0.06 (0.31), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP A 481 HIS 0.003 0.001 HIS B 89 PHE 0.027 0.001 PHE B 97 TYR 0.018 0.001 TYR T 171 ARG 0.005 0.000 ARG A 474 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 607) hydrogen bonds : angle 4.25085 ( 1761) covalent geometry : bond 0.00265 (11347) covalent geometry : angle 0.57932 (15416) *********************** 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 154 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 1.177 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 51 MET cc_start: 0.9280 (tpt) cc_final: 0.8599 (tpp) REVERT: A 133 MET cc_start: 0.9137 (mmp) cc_final: 0.8930 (mmm) REVERT: A 175 MET cc_start: 0.9398 (tpt) cc_final: 0.9120 (tpp) REVERT: A 341 LEU cc_start: 0.9533 (mt) cc_final: 0.9217 (tt) REVERT: A 402 MET cc_start: 0.8519 (mmp) cc_final: 0.8301 (pmm) REVERT: A 575 MET cc_start: 0.9252 (ttt) cc_final: 0.8512 (tpp) REVERT: A 684 MET cc_start: 0.9405 (mmt) cc_final: 0.9085 (tpp) REVERT: A 693 MET cc_start: 0.9524 (mmp) cc_final: 0.9290 (mmp) REVERT: A 708 HIS cc_start: 0.9122 (t70) cc_final: 0.8706 (t-90) REVERT: A 711 LEU cc_start: 0.9583 (mm) cc_final: 0.9291 (mm) REVERT: A 735 LEU cc_start: 0.9624 (mt) cc_final: 0.9424 (mt) REVERT: B 84 LYS cc_start: 0.9664 (tptp) cc_final: 0.9347 (tptp) REVERT: B 92 PHE cc_start: 0.8228 (t80) cc_final: 0.7730 (t80) REVERT: B 162 ASN cc_start: 0.8720 (t0) cc_final: 0.8473 (t0) REVERT: B 202 MET cc_start: 0.9430 (ttp) cc_final: 0.8763 (tmm) REVERT: C 60 ASP cc_start: 0.8782 (m-30) cc_final: 0.8332 (t70) REVERT: C 61 ASP cc_start: 0.8885 (p0) cc_final: 0.8576 (p0) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.2166 time to fit residues: 48.7610 Evaluate side-chains 120 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 64 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 chunk 70 optimal weight: 0.9990 chunk 16 optimal weight: 0.0060 chunk 90 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.9400 ------------------------------------------------------------------------------- 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 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN C 125 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.042623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.030107 restraints weight = 95769.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.031243 restraints weight = 64870.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.032072 restraints weight = 48793.776| |-----------------------------------------------------------------------------| r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3000 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= 0.104 Angle : 0.582 8.247 15416 Z= 0.277 Chirality : 0.039 0.149 1766 Planarity : 0.003 0.028 1977 Dihedral : 5.400 67.531 1593 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.23), residues: 1418 helix: 2.40 (0.19), residues: 749 sheet: 0.37 (0.36), residues: 201 loop : 0.12 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP A 481 HIS 0.003 0.000 HIS B 89 PHE 0.025 0.001 PHE B 97 TYR 0.007 0.001 TYR T 143 ARG 0.003 0.000 ARG T 134 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 607) hydrogen bonds : angle 4.11355 ( 1761) covalent geometry : bond 0.00215 (11347) covalent geometry : angle 0.58178 (15416) *********************** 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 157 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.203 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 51 MET cc_start: 0.9280 (tpt) cc_final: 0.8585 (tpp) REVERT: A 207 ASP cc_start: 0.9513 (t70) cc_final: 0.9182 (p0) REVERT: A 263 MET cc_start: 0.9118 (ppp) cc_final: 0.8900 (ppp) REVERT: A 278 LYS cc_start: 0.9581 (tptp) cc_final: 0.9373 (tppt) REVERT: A 341 LEU cc_start: 0.9515 (mt) cc_final: 0.9132 (tt) REVERT: A 402 MET cc_start: 0.8525 (mmp) cc_final: 0.8313 (pmm) REVERT: A 575 MET cc_start: 0.9225 (ttt) cc_final: 0.8431 (tpp) REVERT: A 669 GLN cc_start: 0.9345 (mm110) cc_final: 0.9130 (mm110) REVERT: A 693 MET cc_start: 0.9527 (mmp) cc_final: 0.9291 (mmp) REVERT: A 704 MET cc_start: 0.9467 (mmm) cc_final: 0.9252 (mmm) REVERT: A 708 HIS cc_start: 0.9049 (t70) cc_final: 0.8665 (t-90) REVERT: A 711 LEU cc_start: 0.9560 (mm) cc_final: 0.9352 (mm) REVERT: A 741 LEU cc_start: 0.9555 (tt) cc_final: 0.9330 (pp) REVERT: B 84 LYS cc_start: 0.9651 (tptp) cc_final: 0.9322 (tptp) REVERT: B 92 PHE cc_start: 0.8183 (t80) cc_final: 0.7674 (t80) REVERT: B 157 LEU cc_start: 0.9675 (mm) cc_final: 0.9355 (mm) REVERT: B 161 PHE cc_start: 0.8972 (m-10) cc_final: 0.8719 (m-80) REVERT: B 162 ASN cc_start: 0.8644 (t0) cc_final: 0.8436 (t0) REVERT: B 202 MET cc_start: 0.9439 (ttp) cc_final: 0.8766 (tmm) REVERT: C 60 ASP cc_start: 0.8758 (m-30) cc_final: 0.8374 (t70) REVERT: C 61 ASP cc_start: 0.8897 (p0) cc_final: 0.8607 (p0) REVERT: C 131 LEU cc_start: 0.9367 (mt) cc_final: 0.9068 (pp) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.2298 time to fit residues: 52.3759 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 : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 131 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 128 optimal weight: 0.0770 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN A 699 GLN B 5 ASN ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.042225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.029825 restraints weight = 95011.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.030929 restraints weight = 64455.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.031700 restraints weight = 48678.686| |-----------------------------------------------------------------------------| r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11347 Z= 0.112 Angle : 0.587 8.225 15416 Z= 0.278 Chirality : 0.039 0.154 1766 Planarity : 0.003 0.027 1977 Dihedral : 5.371 66.654 1593 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.23), residues: 1418 helix: 2.38 (0.19), residues: 749 sheet: 0.40 (0.36), residues: 201 loop : 0.13 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A 481 HIS 0.003 0.001 HIS B 89 PHE 0.025 0.001 PHE B 97 TYR 0.008 0.001 TYR T 143 ARG 0.003 0.000 ARG A 445 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 607) hydrogen bonds : angle 4.13136 ( 1761) covalent geometry : bond 0.00238 (11347) covalent geometry : angle 0.58699 (15416) *********************** 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 155 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.364 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 22 LEU cc_start: 0.9698 (mm) cc_final: 0.9415 (tp) REVERT: A 51 MET cc_start: 0.9306 (tpt) cc_final: 0.8591 (tpp) REVERT: A 133 MET cc_start: 0.9213 (mmp) cc_final: 0.8906 (mmm) REVERT: A 207 ASP cc_start: 0.9522 (t70) cc_final: 0.9202 (p0) REVERT: A 263 MET cc_start: 0.9145 (ppp) cc_final: 0.8934 (ppp) REVERT: A 341 LEU cc_start: 0.9526 (mt) cc_final: 0.9126 (tt) REVERT: A 402 MET cc_start: 0.8567 (mmp) cc_final: 0.8322 (pmm) REVERT: A 575 MET cc_start: 0.9244 (ttt) cc_final: 0.8485 (tpp) REVERT: A 669 GLN cc_start: 0.9332 (mm110) cc_final: 0.9127 (mm110) REVERT: A 693 MET cc_start: 0.9526 (mmp) cc_final: 0.9292 (mmp) REVERT: A 704 MET cc_start: 0.9455 (mmm) cc_final: 0.9232 (mmm) REVERT: A 708 HIS cc_start: 0.9072 (t70) cc_final: 0.8697 (t-90) REVERT: A 711 LEU cc_start: 0.9565 (mm) cc_final: 0.9341 (mm) REVERT: A 741 LEU cc_start: 0.9565 (tt) cc_final: 0.9337 (pp) REVERT: B 84 LYS cc_start: 0.9648 (tptp) cc_final: 0.9328 (tptp) REVERT: B 92 PHE cc_start: 0.8194 (t80) cc_final: 0.7692 (t80) REVERT: B 162 ASN cc_start: 0.8647 (t0) cc_final: 0.8399 (t0) REVERT: B 202 MET cc_start: 0.9446 (ttp) cc_final: 0.8773 (tmm) REVERT: C 60 ASP cc_start: 0.8753 (m-30) cc_final: 0.8357 (t70) REVERT: C 61 ASP cc_start: 0.8874 (p0) cc_final: 0.8604 (p0) REVERT: C 77 MET cc_start: 0.8600 (mtm) cc_final: 0.8248 (ptp) REVERT: C 131 LEU cc_start: 0.9411 (mt) cc_final: 0.9091 (pp) REVERT: T 43 MET cc_start: 0.8158 (ptt) cc_final: 0.7893 (ppp) REVERT: T 127 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8473 (tm-30) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2452 time to fit residues: 54.4517 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 : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 27 optimal weight: 0.0770 chunk 45 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 121 optimal weight: 30.0000 chunk 100 optimal weight: 5.9990 overall best weight: 3.5944 ------------------------------------------------------------------------------- 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 456 GLN ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN C 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.041477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.029261 restraints weight = 97088.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.030337 restraints weight = 65711.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.031139 restraints weight = 49583.306| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3276 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= 0.152 Angle : 0.604 8.044 15416 Z= 0.293 Chirality : 0.039 0.166 1766 Planarity : 0.003 0.027 1977 Dihedral : 5.496 68.011 1593 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.23), residues: 1418 helix: 2.37 (0.19), residues: 742 sheet: 0.33 (0.36), residues: 201 loop : 0.08 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 481 HIS 0.008 0.001 HIS C 89 PHE 0.025 0.002 PHE C 169 TYR 0.012 0.001 TYR T 171 ARG 0.004 0.000 ARG A 445 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 607) hydrogen bonds : angle 4.27356 ( 1761) covalent geometry : bond 0.00315 (11347) covalent geometry : angle 0.60373 (15416) ********************** 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 148 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.192 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: A 51 MET cc_start: 0.9365 (tpt) cc_final: 0.8641 (tpp) REVERT: A 341 LEU cc_start: 0.9537 (mt) cc_final: 0.9142 (tt) REVERT: A 402 MET cc_start: 0.8505 (mmp) cc_final: 0.8293 (pmm) REVERT: A 575 MET cc_start: 0.9254 (ttt) cc_final: 0.8521 (tpp) REVERT: A 693 MET cc_start: 0.9534 (mmp) cc_final: 0.9297 (mmp) REVERT: A 708 HIS cc_start: 0.9171 (t70) cc_final: 0.8646 (t-90) REVERT: A 711 LEU cc_start: 0.9559 (mm) cc_final: 0.9329 (mm) REVERT: B 84 LYS cc_start: 0.9662 (tptp) cc_final: 0.9344 (tptp) REVERT: B 92 PHE cc_start: 0.8274 (t80) cc_final: 0.7791 (t80) REVERT: B 162 ASN cc_start: 0.8677 (t0) cc_final: 0.8431 (t0) REVERT: B 202 MET cc_start: 0.9455 (ttp) cc_final: 0.8866 (tmm) REVERT: C 60 ASP cc_start: 0.8710 (m-30) cc_final: 0.8427 (t0) REVERT: C 61 ASP cc_start: 0.8902 (p0) cc_final: 0.8664 (p0) REVERT: C 77 MET cc_start: 0.8741 (mtm) cc_final: 0.8365 (ptp) REVERT: C 202 MET cc_start: 0.8679 (tmm) cc_final: 0.8430 (tmm) REVERT: T 127 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8523 (tm-30) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2215 time to fit residues: 47.6099 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 : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 92 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 111 optimal weight: 0.0670 chunk 49 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 37 optimal weight: 0.0770 chunk 16 optimal weight: 0.0970 chunk 119 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 overall best weight: 1.4276 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.042283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.029793 restraints weight = 94116.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.030894 restraints weight = 63903.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.031701 restraints weight = 48382.766| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3338 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= 0.106 Angle : 0.586 8.582 15416 Z= 0.277 Chirality : 0.039 0.148 1766 Planarity : 0.003 0.028 1977 Dihedral : 5.439 69.092 1593 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.23), residues: 1418 helix: 2.37 (0.19), residues: 741 sheet: 0.37 (0.36), residues: 201 loop : 0.08 (0.31), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 481 HIS 0.003 0.001 HIS B 89 PHE 0.023 0.001 PHE B 97 TYR 0.008 0.001 TYR T 143 ARG 0.003 0.000 ARG A 445 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 607) hydrogen bonds : angle 4.13080 ( 1761) covalent geometry : bond 0.00223 (11347) covalent geometry : angle 0.58606 (15416) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3366.23 seconds wall clock time: 59 minutes 11.46 seconds (3551.46 seconds total)