Starting phenix.real_space_refine on Tue Feb 11 01:05:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qes_13939/02_2025/7qes_13939.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qes_13939/02_2025/7qes_13939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qes_13939/02_2025/7qes_13939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qes_13939/02_2025/7qes_13939.map" model { file = "/net/cci-nas-00/data/ceres_data/7qes_13939/02_2025/7qes_13939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qes_13939/02_2025/7qes_13939.cif" } resolution = 2.6 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 2066 2.51 5 N 472 2.21 5 O 509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3076 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1494 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "B" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1483 Classifications: {'peptide': 182} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 175} Chain breaks: 1 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 40 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 2.71, per 1000 atoms: 0.88 Number of scatterers: 3076 At special positions: 0 Unit cell: (70.85, 66.49, 85.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 509 8.00 N 472 7.00 C 2066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 169 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 432.9 milliseconds 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 700 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 2 sheets defined 75.4% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 removed outlier: 3.766A pdb=" N ILE A 9 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 15 " --> pdb=" O GLY A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 39 removed outlier: 3.912A pdb=" N ILE A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 39 " --> pdb=" O ILE A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 43 Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 97 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 132 through 159 Processing helix chain 'A' and resid 184 through 217 Processing helix chain 'B' and resid 10 through 15 removed outlier: 3.961A pdb=" N LYS B 15 " --> pdb=" O GLY B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 39 removed outlier: 4.336A pdb=" N LEU B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N THR B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 removed outlier: 4.209A pdb=" N TRP B 44 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY B 45 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASP B 46 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 47 " --> pdb=" O TRP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 101 Proline residue: B 87 - end of helix removed outlier: 3.520A pdb=" N ALA B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 138 Processing helix chain 'B' and resid 138 through 159 removed outlier: 3.582A pdb=" N ILE B 145 " --> pdb=" O PHE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 215 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 206 hydrogen bonds defined for protein. 600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.82 Time building geometry restraints manager: 0.97 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: 872 1.34 - 1.46: 847 1.46 - 1.58: 1378 1.58 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 3139 Sorted by residual: bond pdb=" C1 LMT A 304 " pdb=" C2 LMT A 304 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.04e+00 bond pdb=" C1 LMT B 302 " pdb=" C2 LMT B 302 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" C7 LMT B 301 " pdb=" C8 LMT B 301 " ideal model delta sigma weight residual 1.529 1.567 -0.038 2.00e-02 2.50e+03 3.64e+00 bond pdb=" C7 LMT A 305 " pdb=" C8 LMT A 305 " ideal model delta sigma weight residual 1.529 1.567 -0.038 2.00e-02 2.50e+03 3.63e+00 bond pdb=" C7 LMT B 304 " pdb=" C8 LMT B 304 " ideal model delta sigma weight residual 1.529 1.567 -0.038 2.00e-02 2.50e+03 3.61e+00 ... (remaining 3134 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 4085 1.60 - 3.20: 85 3.20 - 4.80: 28 4.80 - 6.39: 26 6.39 - 7.99: 15 Bond angle restraints: 4239 Sorted by residual: angle pdb=" C6 LMT B 302 " pdb=" C7 LMT B 302 " pdb=" C8 LMT B 302 " ideal model delta sigma weight residual 117.26 109.27 7.99 3.00e+00 1.11e-01 7.10e+00 angle pdb=" C6 LMT B 301 " pdb=" C7 LMT B 301 " pdb=" C8 LMT B 301 " ideal model delta sigma weight residual 117.26 109.49 7.77 3.00e+00 1.11e-01 6.71e+00 angle pdb=" C6 LMT A 301 " pdb=" C7 LMT A 301 " pdb=" C8 LMT A 301 " ideal model delta sigma weight residual 117.26 109.56 7.70 3.00e+00 1.11e-01 6.59e+00 angle pdb=" C6 LMT B 304 " pdb=" C7 LMT B 304 " pdb=" C8 LMT B 304 " ideal model delta sigma weight residual 117.26 109.68 7.58 3.00e+00 1.11e-01 6.39e+00 angle pdb=" C2 LMT B 304 " pdb=" C3 LMT B 304 " pdb=" C4 LMT B 304 " ideal model delta sigma weight residual 117.09 109.52 7.57 3.00e+00 1.11e-01 6.37e+00 ... (remaining 4234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.82: 1486 11.82 - 23.63: 223 23.63 - 35.45: 68 35.45 - 47.26: 26 47.26 - 59.08: 12 Dihedral angle restraints: 1815 sinusoidal: 735 harmonic: 1080 Sorted by residual: dihedral pdb=" CA PRO B 175 " pdb=" C PRO B 175 " pdb=" N ASN B 176 " pdb=" CA ASN B 176 " ideal model delta harmonic sigma weight residual -180.00 -159.26 -20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA PRO A 175 " pdb=" C PRO A 175 " pdb=" N ASN A 176 " pdb=" CA ASN A 176 " ideal model delta harmonic sigma weight residual -180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLU A 42 " pdb=" C GLU A 42 " pdb=" N VAL A 43 " pdb=" CA VAL A 43 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 1812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 291 0.032 - 0.064: 135 0.064 - 0.095: 39 0.095 - 0.127: 12 0.127 - 0.159: 2 Chirality restraints: 479 Sorted by residual: chirality pdb=" CA THR B 86 " pdb=" N THR B 86 " pdb=" C THR B 86 " pdb=" CB THR B 86 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" CA THR A 86 " pdb=" N THR A 86 " pdb=" C THR A 86 " pdb=" CB THR A 86 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" CA PRO B 185 " pdb=" N PRO B 185 " pdb=" C PRO B 185 " pdb=" CB PRO B 185 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.27e-01 ... (remaining 476 not shown) Planarity restraints: 500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 174 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO A 175 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 175 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 175 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 86 " 0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO B 87 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 87 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 87 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 57 " 0.012 5.00e-02 4.00e+02 1.83e-02 5.33e-01 pdb=" N PRO A 58 " -0.032 5.00e-02 4.00e+02 pdb=" CA PRO A 58 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 58 " 0.010 5.00e-02 4.00e+02 ... (remaining 497 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 29 2.68 - 3.23: 2894 3.23 - 3.79: 4300 3.79 - 4.34: 5872 4.34 - 4.90: 9832 Nonbonded interactions: 22927 Sorted by model distance: nonbonded pdb=" O ILE B 71 " pdb=" OH TYR B 158 " model vdw 2.122 3.040 nonbonded pdb=" O ILE A 71 " pdb=" OH TYR A 158 " model vdw 2.154 3.040 nonbonded pdb=" OH TYR B 68 " pdb=" O LYS B 168 " model vdw 2.278 3.040 nonbonded pdb=" OH TYR A 68 " pdb=" O LYS A 168 " model vdw 2.296 3.040 nonbonded pdb=" OD1 ASP A 66 " pdb=" O HOH A 401 " model vdw 2.335 3.040 ... (remaining 22922 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 'A' and (resid 9 through 217 or resid 301 through 302 or (resid 304 and ( \ name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 )))) selection = (chain 'B' and (resid 9 through 97 or resid 131 through 217 or (resid 301 and (n \ ame C3 or name C4 or name C5 or name C6 or name C7 or name C8 )) or (resid 302 a \ nd (name C5 or name C6 or name C7 )) or resid 304)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.800 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:14.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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 : 0.006 0.049 3139 Z= 0.383 Angle : 0.860 7.993 4239 Z= 0.375 Chirality : 0.041 0.159 479 Planarity : 0.003 0.036 500 Dihedral : 13.928 59.078 1097 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -0.99 (0.41), residues: 358 helix: -0.23 (0.31), residues: 238 sheet: 0.44 (0.95), residues: 28 loop : -1.85 (0.62), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 134 HIS 0.002 0.001 HIS A 73 PHE 0.010 0.001 PHE A 181 TYR 0.009 0.001 TYR B 65 ARG 0.005 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.357 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 1.3746 time to fit residues: 42.6061 Evaluate side-chains 24 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 40.0000 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.088530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.060385 restraints weight = 7958.055| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.41 r_work: 0.2876 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3139 Z= 0.199 Angle : 0.613 6.509 4239 Z= 0.335 Chirality : 0.042 0.157 479 Planarity : 0.004 0.035 500 Dihedral : 9.782 59.204 443 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.30 % Allowed : 7.32 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.22 (0.44), residues: 358 helix: 1.77 (0.33), residues: 239 sheet: 1.38 (1.09), residues: 22 loop : -1.86 (0.60), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 133 HIS 0.002 0.001 HIS A 94 PHE 0.011 0.001 PHE A 31 TYR 0.010 0.002 TYR B 212 ARG 0.002 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.366 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 1.2548 time to fit residues: 41.4793 Evaluate side-chains 27 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.090166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.062291 restraints weight = 7751.925| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.36 r_work: 0.2914 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3139 Z= 0.168 Angle : 0.539 6.420 4239 Z= 0.292 Chirality : 0.041 0.165 479 Planarity : 0.004 0.031 500 Dihedral : 8.707 57.699 443 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.22 % Allowed : 10.67 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.00 (0.45), residues: 358 helix: 2.56 (0.33), residues: 239 sheet: 1.45 (1.09), residues: 22 loop : -2.10 (0.58), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 133 HIS 0.002 0.001 HIS B 16 PHE 0.010 0.001 PHE A 31 TYR 0.017 0.002 TYR B 158 ARG 0.001 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.277 Fit side-chains REVERT: A 212 TYR cc_start: 0.6636 (OUTLIER) cc_final: 0.6006 (t80) REVERT: B 16 HIS cc_start: 0.5970 (t70) cc_final: 0.5526 (t70) REVERT: B 97 TYR cc_start: 0.5055 (t80) cc_final: 0.4727 (t80) outliers start: 4 outliers final: 0 residues processed: 31 average time/residue: 1.2857 time to fit residues: 41.1212 Evaluate side-chains 27 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 27 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.088967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.060446 restraints weight = 7884.755| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.39 r_work: 0.2872 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3139 Z= 0.261 Angle : 0.600 8.016 4239 Z= 0.321 Chirality : 0.042 0.172 479 Planarity : 0.004 0.034 500 Dihedral : 8.675 58.548 443 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.44 % Allowed : 10.37 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.20 (0.45), residues: 358 helix: 2.72 (0.32), residues: 239 sheet: 1.34 (1.08), residues: 22 loop : -1.98 (0.61), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 133 HIS 0.002 0.001 HIS A 73 PHE 0.010 0.001 PHE A 31 TYR 0.011 0.002 TYR B 65 ARG 0.003 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.332 Fit side-chains REVERT: A 136 TYR cc_start: 0.6900 (OUTLIER) cc_final: 0.6529 (m-80) REVERT: A 212 TYR cc_start: 0.6662 (OUTLIER) cc_final: 0.6009 (t80) REVERT: B 97 TYR cc_start: 0.4978 (t80) cc_final: 0.4729 (t80) REVERT: B 101 GLU cc_start: 0.5063 (OUTLIER) cc_final: 0.4685 (pt0) REVERT: B 136 TYR cc_start: 0.7631 (t80) cc_final: 0.7298 (t80) outliers start: 8 outliers final: 1 residues processed: 31 average time/residue: 1.2389 time to fit residues: 39.7275 Evaluate side-chains 30 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 101 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.088367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.059803 restraints weight = 7880.423| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.40 r_work: 0.2859 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3139 Z= 0.296 Angle : 0.605 6.476 4239 Z= 0.327 Chirality : 0.043 0.173 479 Planarity : 0.004 0.035 500 Dihedral : 8.750 59.440 443 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.44 % Allowed : 12.80 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.25 (0.45), residues: 358 helix: 2.77 (0.32), residues: 239 sheet: 1.27 (1.07), residues: 22 loop : -1.98 (0.61), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 133 HIS 0.002 0.001 HIS A 73 PHE 0.010 0.001 PHE A 31 TYR 0.011 0.002 TYR B 65 ARG 0.003 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.369 Fit side-chains REVERT: A 136 TYR cc_start: 0.6930 (OUTLIER) cc_final: 0.6600 (m-80) REVERT: A 212 TYR cc_start: 0.6642 (OUTLIER) cc_final: 0.5989 (t80) REVERT: B 97 TYR cc_start: 0.4934 (OUTLIER) cc_final: 0.4673 (t80) REVERT: B 101 GLU cc_start: 0.4765 (OUTLIER) cc_final: 0.4318 (pt0) outliers start: 8 outliers final: 1 residues processed: 30 average time/residue: 1.2026 time to fit residues: 37.3818 Evaluate side-chains 31 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 101 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 6 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.089221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.060702 restraints weight = 7933.858| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.39 r_work: 0.2882 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3139 Z= 0.232 Angle : 0.572 6.429 4239 Z= 0.311 Chirality : 0.042 0.170 479 Planarity : 0.004 0.036 500 Dihedral : 8.458 59.623 443 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.44 % Allowed : 14.33 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.37 (0.45), residues: 358 helix: 2.89 (0.32), residues: 239 sheet: 1.34 (1.09), residues: 22 loop : -2.02 (0.60), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 133 HIS 0.014 0.002 HIS B 16 PHE 0.009 0.001 PHE A 31 TYR 0.009 0.001 TYR B 68 ARG 0.002 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.324 Fit side-chains REVERT: A 136 TYR cc_start: 0.7003 (OUTLIER) cc_final: 0.6666 (m-80) REVERT: A 212 TYR cc_start: 0.6530 (OUTLIER) cc_final: 0.5901 (t80) REVERT: B 97 TYR cc_start: 0.5093 (OUTLIER) cc_final: 0.4865 (t80) REVERT: B 101 GLU cc_start: 0.4661 (OUTLIER) cc_final: 0.4279 (pt0) REVERT: B 136 TYR cc_start: 0.7772 (t80) cc_final: 0.7376 (t80) outliers start: 8 outliers final: 1 residues processed: 32 average time/residue: 1.2356 time to fit residues: 40.8476 Evaluate side-chains 31 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 101 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 9 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.089261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.060781 restraints weight = 7842.930| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.40 r_work: 0.2872 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3139 Z= 0.243 Angle : 0.599 8.488 4239 Z= 0.317 Chirality : 0.042 0.172 479 Planarity : 0.004 0.035 500 Dihedral : 8.321 59.721 443 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.83 % Allowed : 15.85 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.43 (0.45), residues: 358 helix: 2.90 (0.32), residues: 240 sheet: 1.32 (1.08), residues: 22 loop : -1.91 (0.61), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 133 HIS 0.002 0.001 HIS B 16 PHE 0.009 0.001 PHE A 31 TYR 0.009 0.002 TYR B 68 ARG 0.002 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.304 Fit side-chains REVERT: A 136 TYR cc_start: 0.6987 (OUTLIER) cc_final: 0.6667 (m-80) REVERT: A 212 TYR cc_start: 0.6510 (OUTLIER) cc_final: 0.5892 (t80) REVERT: B 101 GLU cc_start: 0.4654 (OUTLIER) cc_final: 0.4107 (pt0) outliers start: 6 outliers final: 1 residues processed: 33 average time/residue: 1.2310 time to fit residues: 41.8792 Evaluate side-chains 30 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 101 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.089231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.060834 restraints weight = 7902.326| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.37 r_work: 0.2882 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3139 Z= 0.249 Angle : 0.592 7.442 4239 Z= 0.317 Chirality : 0.042 0.172 479 Planarity : 0.004 0.036 500 Dihedral : 8.236 59.950 443 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.52 % Allowed : 16.77 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.44 (0.45), residues: 358 helix: 2.89 (0.32), residues: 240 sheet: 1.27 (1.07), residues: 22 loop : -1.88 (0.62), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 133 HIS 0.002 0.001 HIS A 73 PHE 0.009 0.001 PHE A 31 TYR 0.025 0.002 TYR B 97 ARG 0.002 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.350 Fit side-chains REVERT: A 136 TYR cc_start: 0.7024 (OUTLIER) cc_final: 0.6717 (m-80) REVERT: A 212 TYR cc_start: 0.6396 (OUTLIER) cc_final: 0.5807 (t80) outliers start: 5 outliers final: 2 residues processed: 30 average time/residue: 1.1722 time to fit residues: 36.4290 Evaluate side-chains 30 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 212 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 0.0970 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.089327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.060942 restraints weight = 7803.048| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.37 r_work: 0.2891 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3139 Z= 0.236 Angle : 0.624 12.800 4239 Z= 0.324 Chirality : 0.041 0.171 479 Planarity : 0.004 0.036 500 Dihedral : 8.112 59.954 443 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.13 % Allowed : 15.85 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.49 (0.45), residues: 358 helix: 2.94 (0.32), residues: 240 sheet: 1.32 (1.08), residues: 22 loop : -1.90 (0.61), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 133 HIS 0.003 0.001 HIS B 16 PHE 0.008 0.001 PHE A 31 TYR 0.024 0.002 TYR B 97 ARG 0.002 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.320 Fit side-chains REVERT: A 136 TYR cc_start: 0.7117 (OUTLIER) cc_final: 0.6806 (m-80) REVERT: A 212 TYR cc_start: 0.6386 (OUTLIER) cc_final: 0.5797 (t80) outliers start: 7 outliers final: 1 residues processed: 32 average time/residue: 1.1849 time to fit residues: 39.2935 Evaluate side-chains 29 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 212 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 0.0970 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 0.0870 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.090818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.062893 restraints weight = 7976.094| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.39 r_work: 0.2944 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3139 Z= 0.167 Angle : 0.572 8.361 4239 Z= 0.307 Chirality : 0.040 0.167 479 Planarity : 0.004 0.036 500 Dihedral : 7.495 58.675 443 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.91 % Allowed : 17.07 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.54 (0.45), residues: 358 helix: 3.01 (0.32), residues: 240 sheet: 1.42 (1.10), residues: 22 loop : -1.97 (0.60), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 133 HIS 0.001 0.000 HIS A 16 PHE 0.009 0.001 PHE A 31 TYR 0.024 0.001 TYR B 97 ARG 0.002 0.000 ARG A 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.348 Fit side-chains REVERT: A 136 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.6764 (m-80) REVERT: A 212 TYR cc_start: 0.6316 (OUTLIER) cc_final: 0.5666 (t80) outliers start: 3 outliers final: 0 residues processed: 29 average time/residue: 1.1721 time to fit residues: 35.2605 Evaluate side-chains 25 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 212 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 0.0970 chunk 11 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.090844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.063009 restraints weight = 7873.876| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.39 r_work: 0.2944 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3139 Z= 0.193 Angle : 0.640 13.990 4239 Z= 0.331 Chirality : 0.040 0.168 479 Planarity : 0.004 0.036 500 Dihedral : 7.280 58.305 443 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.22 % Allowed : 16.46 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.66 (0.45), residues: 358 helix: 3.09 (0.32), residues: 240 sheet: 1.40 (1.10), residues: 22 loop : -1.88 (0.63), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 133 HIS 0.001 0.000 HIS A 73 PHE 0.009 0.001 PHE A 31 TYR 0.024 0.001 TYR B 97 ARG 0.002 0.000 ARG A 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2836.46 seconds wall clock time: 50 minutes 40.86 seconds (3040.86 seconds total)