Starting phenix.real_space_refine on Tue Feb 13 04:24:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qes_13939/02_2024/7qes_13939_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qes_13939/02_2024/7qes_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qes_13939/02_2024/7qes_13939.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qes_13939/02_2024/7qes_13939.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qes_13939/02_2024/7qes_13939_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qes_13939/02_2024/7qes_13939_updated.pdb" } 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 Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 159": "OD1" <-> "OD2" Residue "B PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 187": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 2.43, per 1000 atoms: 0.79 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 - 3.50 Amino acid : False - 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: 1.23 Conformation dependent library (CDL) restraints added in 528.8 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... running ksdssp... Secondary structure from input PDB file: 15 helices and 2 sheets defined 68.6% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 6 through 14 Processing helix chain 'A' and resid 19 through 38 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) Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 73 through 96 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 132 through 158 Processing helix chain 'A' and resid 185 through 216 Processing helix chain 'B' and resid 10 through 14 Processing helix chain 'B' and resid 19 through 38 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) Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'B' and resid 44 through 46 No H-bonds generated for 'chain 'B' and resid 44 through 46' Processing helix chain 'B' and resid 60 through 68 Processing helix chain 'B' and resid 73 through 100 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 158 removed outlier: 3.993A pdb=" N SER B 139 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 145 " --> pdb=" O PHE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 214 Processing sheet with id= A, first strand: chain 'A' and resid 166 through 169 Processing sheet with id= B, first strand: chain 'B' and resid 166 through 169 186 hydrogen bonds defined for protein. 552 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: 0.77 Time building geometry restraints manager: 1.32 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: 100.00 - 106.80: 78 106.80 - 113.60: 1790 113.60 - 120.41: 1216 120.41 - 127.21: 1110 127.21 - 134.01: 45 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: 30 2.68 - 3.23: 2908 3.23 - 3.79: 4322 3.79 - 4.34: 5905 4.34 - 4.90: 9842 Nonbonded interactions: 23007 Sorted by model distance: nonbonded pdb=" O ILE B 71 " pdb=" OH TYR B 158 " model vdw 2.122 2.440 nonbonded pdb=" O ILE A 71 " pdb=" OH TYR A 158 " model vdw 2.154 2.440 nonbonded pdb=" OH TYR B 68 " pdb=" O LYS B 168 " model vdw 2.278 2.440 nonbonded pdb=" OH TYR A 68 " pdb=" O LYS A 168 " model vdw 2.296 2.440 nonbonded pdb=" OD1 ASP A 66 " pdb=" O HOH A 401 " model vdw 2.335 2.440 ... (remaining 23002 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.410 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.960 Find NCS groups from input model: 0.170 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:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.260 ------------------------------------------------------------------------------- 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= 0.390 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 fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.361 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 1.3906 time to fit residues: 43.0530 Evaluate side-chains 24 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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: 0.1980 chunk 27 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3139 Z= 0.178 Angle : 0.575 6.561 4239 Z= 0.307 Chirality : 0.040 0.146 479 Planarity : 0.004 0.033 500 Dihedral : 9.387 59.712 443 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.30 % Allowed : 7.62 % Favored : 92.07 % 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: 1.05 (0.45), residues: 358 helix: 1.66 (0.33), residues: 237 sheet: 0.41 (0.95), residues: 34 loop : -1.92 (0.63), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 133 HIS 0.002 0.001 HIS A 67 PHE 0.009 0.001 PHE A 150 TYR 0.013 0.002 TYR A 155 ARG 0.002 0.000 ARG A 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 32 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.361 Fit side-chains REVERT: B 97 TYR cc_start: 0.5389 (t80) cc_final: 0.5148 (t80) outliers start: 1 outliers final: 0 residues processed: 31 average time/residue: 1.2001 time to fit residues: 38.5502 Evaluate side-chains 26 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 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 18 optimal weight: 30.0000 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 22 optimal weight: 0.4980 chunk 9 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1884 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= 0.211 Angle : 0.546 6.471 4239 Z= 0.291 Chirality : 0.040 0.162 479 Planarity : 0.004 0.038 500 Dihedral : 8.888 58.587 443 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.22 % Allowed : 10.06 % Favored : 88.72 % 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: 1.80 (0.46), residues: 358 helix: 2.40 (0.33), residues: 237 sheet: 0.60 (0.98), residues: 34 loop : -2.16 (0.64), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 133 HIS 0.002 0.001 HIS A 73 PHE 0.011 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 fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.365 Fit side-chains REVERT: B 97 TYR cc_start: 0.5516 (t80) cc_final: 0.5283 (t80) outliers start: 4 outliers final: 1 residues processed: 31 average time/residue: 1.1876 time to fit residues: 38.1415 Evaluate side-chains 28 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 19 optimal weight: 0.4980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3139 Z= 0.191 Angle : 0.538 7.030 4239 Z= 0.283 Chirality : 0.040 0.167 479 Planarity : 0.003 0.033 500 Dihedral : 8.342 57.586 443 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.13 % Allowed : 11.59 % Favored : 86.28 % 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: 2.12 (0.46), residues: 358 helix: 2.72 (0.33), residues: 236 sheet: 0.74 (1.00), residues: 34 loop : -2.25 (0.62), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 133 HIS 0.002 0.001 HIS B 16 PHE 0.009 0.001 PHE A 31 TYR 0.008 0.001 TYR A 158 ARG 0.002 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 35 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 28 time to evaluate : 0.299 Fit side-chains REVERT: A 212 TYR cc_start: 0.6972 (OUTLIER) cc_final: 0.6317 (t80) outliers start: 7 outliers final: 1 residues processed: 33 average time/residue: 1.1362 time to fit residues: 38.8581 Evaluate side-chains 28 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 212 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 30.0000 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3139 Z= 0.199 Angle : 0.528 6.490 4239 Z= 0.280 Chirality : 0.040 0.169 479 Planarity : 0.004 0.033 500 Dihedral : 7.984 57.300 443 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.52 % Allowed : 14.02 % Favored : 84.45 % 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: 2.23 (0.46), residues: 358 helix: 2.83 (0.32), residues: 236 sheet: 0.80 (1.02), residues: 34 loop : -2.29 (0.61), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 133 HIS 0.001 0.000 HIS A 94 PHE 0.009 0.001 PHE A 31 TYR 0.008 0.001 TYR B 158 ARG 0.002 0.000 ARG A 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 32 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 27 time to evaluate : 0.366 Fit side-chains REVERT: A 136 TYR cc_start: 0.6842 (OUTLIER) cc_final: 0.6504 (m-80) REVERT: A 212 TYR cc_start: 0.6866 (OUTLIER) cc_final: 0.6245 (t80) outliers start: 5 outliers final: 1 residues processed: 31 average time/residue: 1.1139 time to fit residues: 35.8423 Evaluate side-chains 29 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 212 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3139 Z= 0.184 Angle : 0.546 10.346 4239 Z= 0.282 Chirality : 0.040 0.168 479 Planarity : 0.003 0.033 500 Dihedral : 7.586 56.715 443 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.83 % Allowed : 14.33 % Favored : 83.84 % 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: 2.39 (0.45), residues: 358 helix: 2.91 (0.32), residues: 236 sheet: 1.18 (1.10), residues: 28 loop : -2.04 (0.60), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 133 HIS 0.001 0.000 HIS B 73 PHE 0.008 0.001 PHE A 31 TYR 0.017 0.001 TYR B 97 ARG 0.002 0.000 ARG A 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 33 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 27 time to evaluate : 0.365 Fit side-chains REVERT: A 136 TYR cc_start: 0.6836 (OUTLIER) cc_final: 0.6487 (m-80) REVERT: A 212 TYR cc_start: 0.6815 (OUTLIER) cc_final: 0.6210 (t80) outliers start: 6 outliers final: 2 residues processed: 32 average time/residue: 1.1276 time to fit residues: 37.4458 Evaluate side-chains 31 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 199 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3139 Z= 0.204 Angle : 0.551 7.863 4239 Z= 0.291 Chirality : 0.040 0.169 479 Planarity : 0.004 0.032 500 Dihedral : 7.399 56.567 443 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.74 % Allowed : 14.02 % 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: 2.40 (0.45), residues: 358 helix: 2.85 (0.32), residues: 237 sheet: 1.19 (1.10), residues: 28 loop : -1.88 (0.62), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 133 HIS 0.001 0.000 HIS B 16 PHE 0.010 0.001 PHE A 31 TYR 0.009 0.001 TYR B 158 ARG 0.002 0.000 ARG A 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 37 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 28 time to evaluate : 0.361 Fit side-chains REVERT: A 136 TYR cc_start: 0.6935 (OUTLIER) cc_final: 0.6577 (m-80) REVERT: A 212 TYR cc_start: 0.6725 (OUTLIER) cc_final: 0.6019 (t80) outliers start: 9 outliers final: 2 residues processed: 36 average time/residue: 1.0781 time to fit residues: 40.2599 Evaluate side-chains 31 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 199 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2583 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= 0.191 Angle : 0.591 11.369 4239 Z= 0.304 Chirality : 0.040 0.168 479 Planarity : 0.004 0.033 500 Dihedral : 7.203 56.056 443 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.83 % Allowed : 14.94 % 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: 2.42 (0.45), residues: 358 helix: 2.86 (0.32), residues: 237 sheet: 1.24 (1.10), residues: 28 loop : -1.85 (0.62), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 133 HIS 0.001 0.001 HIS B 16 PHE 0.008 0.001 PHE A 31 TYR 0.024 0.001 TYR B 97 ARG 0.002 0.000 ARG A 32 *********************** 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 32 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 0.284 Fit side-chains REVERT: A 136 TYR cc_start: 0.6934 (OUTLIER) cc_final: 0.6610 (m-80) REVERT: A 212 TYR cc_start: 0.6651 (OUTLIER) cc_final: 0.6008 (t80) outliers start: 6 outliers final: 2 residues processed: 32 average time/residue: 1.1517 time to fit residues: 38.1767 Evaluate side-chains 29 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 25 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 138 SER 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 29 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2701 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= 0.193 Angle : 0.575 8.523 4239 Z= 0.303 Chirality : 0.040 0.168 479 Planarity : 0.004 0.033 500 Dihedral : 7.065 55.523 443 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.83 % Allowed : 15.24 % Favored : 82.93 % 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: 236 sheet: 1.24 (1.10), residues: 28 loop : -1.89 (0.62), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 133 HIS 0.001 0.000 HIS B 73 PHE 0.009 0.001 PHE A 31 TYR 0.022 0.002 TYR B 97 ARG 0.003 0.000 ARG B 98 *********************** 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 32 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 136 TYR cc_start: 0.6985 (OUTLIER) cc_final: 0.6667 (m-80) REVERT: A 212 TYR cc_start: 0.6593 (OUTLIER) cc_final: 0.5981 (t80) outliers start: 6 outliers final: 4 residues processed: 31 average time/residue: 1.1020 time to fit residues: 35.5047 Evaluate side-chains 32 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 138 SER Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 97 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 0.0050 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3139 Z= 0.179 Angle : 0.604 12.802 4239 Z= 0.308 Chirality : 0.039 0.168 479 Planarity : 0.003 0.033 500 Dihedral : 6.799 54.242 443 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.83 % Allowed : 15.55 % Favored : 82.62 % 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: 2.57 (0.46), residues: 358 helix: 2.94 (0.32), residues: 236 sheet: 1.91 (1.18), residues: 22 loop : -1.63 (0.62), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 133 HIS 0.001 0.000 HIS B 73 PHE 0.008 0.001 PHE A 31 TYR 0.012 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 32 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 136 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.6657 (m-80) REVERT: A 212 TYR cc_start: 0.6554 (OUTLIER) cc_final: 0.5950 (t80) outliers start: 6 outliers final: 4 residues processed: 31 average time/residue: 1.0825 time to fit residues: 34.8680 Evaluate side-chains 31 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 25 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 138 SER Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 97 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 0.0670 chunk 25 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 0.0770 chunk 19 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.091226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.063036 restraints weight = 7917.851| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.37 r_work: 0.2929 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3139 Z= 0.173 Angle : 0.565 8.324 4239 Z= 0.296 Chirality : 0.039 0.168 479 Planarity : 0.003 0.033 500 Dihedral : 6.652 52.798 443 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % 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: 2.58 (0.45), residues: 358 helix: 2.94 (0.32), residues: 236 sheet: 1.92 (1.18), residues: 22 loop : -1.58 (0.61), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 133 HIS 0.001 0.000 HIS B 67 PHE 0.009 0.001 PHE A 31 TYR 0.010 0.001 TYR B 97 ARG 0.001 0.000 ARG A 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1372.11 seconds wall clock time: 25 minutes 5.28 seconds (1505.28 seconds total)