Starting phenix.real_space_refine on Tue Feb 11 00:20:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qeu_13941/02_2025/7qeu_13941.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qeu_13941/02_2025/7qeu_13941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qeu_13941/02_2025/7qeu_13941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qeu_13941/02_2025/7qeu_13941.map" model { file = "/net/cci-nas-00/data/ceres_data/7qeu_13941/02_2025/7qeu_13941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qeu_13941/02_2025/7qeu_13941.cif" } resolution = 2.7 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 28 5.16 5 C 2011 2.51 5 N 468 2.21 5 O 495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 3002 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1419 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "B" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1514 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {'LMT': 2, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {'LMT': 2, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 2.63, per 1000 atoms: 0.88 Number of scatterers: 3002 At special positions: 0 Unit cell: (71.94, 67.58, 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 28 16.00 O 495 8.00 N 468 7.00 C 2011 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: 1.03 Conformation dependent library (CDL) restraints added in 401.9 milliseconds 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 690 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 2 sheets defined 77.2% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 23 through 39 removed outlier: 3.561A 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 101 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 130 through 159 removed outlier: 3.557A pdb=" N VAL A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 217 removed outlier: 3.647A pdb=" N ARG A 216 " --> pdb=" O TYR A 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 15 removed outlier: 3.703A pdb=" N VAL B 13 " --> pdb=" O ILE B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 39 removed outlier: 3.850A pdb=" N ILE B 23 " --> pdb=" O SER B 19 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N THR B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 removed outlier: 3.532A pdb=" N TRP B 44 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY B 45 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASP B 46 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 3.677A 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 Processing helix chain 'B' and resid 130 through 159 removed outlier: 3.519A pdb=" N VAL B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 217 removed outlier: 3.518A pdb=" N ARG B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) 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 53 215 hydrogen bonds defined for protein. 627 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: 0.78 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 865 1.34 - 1.46: 666 1.46 - 1.57: 1502 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 3073 Sorted by residual: bond pdb=" C1 LMT A 301 " pdb=" C2 LMT A 301 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.09e+00 bond pdb=" C1 LMT B 402 " pdb=" C2 LMT B 402 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.00e-02 2.50e+03 5.85e+00 bond pdb=" C7 LMT B 401 " pdb=" C8 LMT B 401 " 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 302 " pdb=" C8 LMT A 302 " ideal model delta sigma weight residual 1.529 1.566 -0.037 2.00e-02 2.50e+03 3.44e+00 bond pdb=" C7 LMT B 402 " pdb=" C8 LMT B 402 " ideal model delta sigma weight residual 1.529 1.565 -0.036 2.00e-02 2.50e+03 3.27e+00 ... (remaining 3068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 4005 1.57 - 3.13: 97 3.13 - 4.70: 28 4.70 - 6.27: 19 6.27 - 7.83: 10 Bond angle restraints: 4159 Sorted by residual: angle pdb=" C6 LMT A 302 " pdb=" C7 LMT A 302 " pdb=" C8 LMT A 302 " ideal model delta sigma weight residual 117.26 109.43 7.83 3.00e+00 1.11e-01 6.82e+00 angle pdb=" C6 LMT B 402 " pdb=" C7 LMT B 402 " pdb=" C8 LMT B 402 " 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 117.26 109.62 7.64 3.00e+00 1.11e-01 6.48e+00 angle pdb=" CA ARG B 75 " pdb=" CB ARG B 75 " pdb=" CG ARG B 75 " ideal model delta sigma weight residual 114.10 109.10 5.00 2.00e+00 2.50e-01 6.26e+00 angle pdb=" C6 LMT B 401 " pdb=" C7 LMT B 401 " pdb=" C8 LMT B 401 " ideal model delta sigma weight residual 117.26 109.76 7.50 3.00e+00 1.11e-01 6.25e+00 ... (remaining 4154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.67: 1470 11.67 - 23.33: 199 23.33 - 35.00: 87 35.00 - 46.67: 18 46.67 - 58.33: 9 Dihedral angle restraints: 1783 sinusoidal: 720 harmonic: 1063 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 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+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 -159.81 -20.19 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CB MET B 34 " pdb=" CG MET B 34 " pdb=" SD MET B 34 " pdb=" CE MET B 34 " ideal model delta sinusoidal sigma weight residual 180.00 123.06 56.94 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 1780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 220 0.028 - 0.055: 174 0.055 - 0.082: 48 0.082 - 0.110: 22 0.110 - 0.137: 7 Chirality restraints: 471 Sorted by residual: 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 2.39 0.14 2.00e-01 2.50e+01 4.69e-01 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 2.39 0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA PRO B 173 " pdb=" N PRO B 173 " pdb=" C PRO B 173 " pdb=" CB PRO B 173 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 468 not shown) Planarity restraints: 494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 174 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO A 175 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 175 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 175 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 65 " -0.014 2.00e-02 2.50e+03 7.43e-03 1.10e+00 pdb=" CG TYR B 65 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR B 65 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 65 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 65 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 65 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 65 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 65 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 174 " -0.015 5.00e-02 4.00e+02 2.32e-02 8.63e-01 pdb=" N PRO B 175 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO B 175 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 175 " -0.013 5.00e-02 4.00e+02 ... (remaining 491 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 36 2.69 - 3.24: 2959 3.24 - 3.79: 4382 3.79 - 4.35: 5680 4.35 - 4.90: 9613 Nonbonded interactions: 22670 Sorted by model distance: nonbonded pdb=" O ILE B 71 " pdb=" OH TYR B 158 " model vdw 2.135 3.040 nonbonded pdb=" O ILE A 71 " pdb=" OH TYR A 158 " model vdw 2.140 3.040 nonbonded pdb=" OH TYR A 68 " pdb=" O LYS A 168 " model vdw 2.260 3.040 nonbonded pdb=" O CYS A 174 " pdb=" O HOH A 401 " model vdw 2.291 3.040 nonbonded pdb=" O THR B 135 " pdb=" OG SER B 138 " model vdw 2.295 3.040 ... (remaining 22665 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 18 through 217 or (resid 301 and (name C4 or name C5 or na \ me C6 or name C7 or name C8 )) or resid 302 through 303)) selection = (chain 'B' and (resid 18 through 217 or resid 401 or (resid 402 and (name C3 or \ name C4 or name C5 or name C6 or name C7 or name C8 )) or (resid 403 and (name C \ 11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C18 or na \ me C19 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C8 )))) } 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: 0.280 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.760 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 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 : 0.007 0.049 3073 Z= 0.485 Angle : 0.798 7.832 4159 Z= 0.375 Chirality : 0.043 0.137 471 Planarity : 0.003 0.029 494 Dihedral : 13.541 58.333 1075 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % 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: 0.76 (0.43), residues: 351 helix: 0.99 (0.32), residues: 236 sheet: 1.25 (1.08), residues: 22 loop : -0.78 (0.67), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 24 HIS 0.002 0.001 HIS A 73 PHE 0.013 0.001 PHE A 181 TYR 0.014 0.002 TYR B 65 ARG 0.003 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.342 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 1.4858 time to fit residues: 54.8136 Evaluate side-chains 30 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.0670 chunk 21 optimal weight: 0.9990 overall best weight: 0.9924 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.081967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.057588 restraints weight = 7937.600| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.38 r_work: 0.2809 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3073 Z= 0.219 Angle : 0.579 6.746 4159 Z= 0.322 Chirality : 0.043 0.139 471 Planarity : 0.004 0.031 494 Dihedral : 7.406 52.210 426 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.24 % Allowed : 7.74 % Favored : 91.02 % 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: 2.60 (0.45), residues: 351 helix: 2.62 (0.32), residues: 246 sheet: 1.39 (1.10), residues: 22 loop : -1.07 (0.70), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 133 HIS 0.003 0.001 HIS B 94 PHE 0.010 0.001 PHE B 31 TYR 0.009 0.002 TYR B 212 ARG 0.007 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8302 (mm-30) REVERT: A 216 ARG cc_start: 0.8488 (ttp80) cc_final: 0.7947 (tmt170) REVERT: B 42 GLU cc_start: 0.6812 (pp20) cc_final: 0.6487 (pp20) outliers start: 4 outliers final: 1 residues processed: 41 average time/residue: 1.3166 time to fit residues: 55.5414 Evaluate side-chains 33 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.082131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.057685 restraints weight = 7790.020| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.41 r_work: 0.2796 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 3073 Z= 0.239 Angle : 0.536 6.379 4159 Z= 0.293 Chirality : 0.042 0.146 471 Planarity : 0.003 0.029 494 Dihedral : 6.377 41.567 426 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.24 % Allowed : 12.07 % Favored : 86.69 % 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: 2.97 (0.46), residues: 351 helix: 2.98 (0.32), residues: 245 sheet: 1.66 (1.15), residues: 22 loop : -1.24 (0.69), residues: 84 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 0.010 0.001 PHE B 31 TYR 0.010 0.001 TYR A 158 ARG 0.004 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: B 93 MET cc_start: 0.8429 (ttm) cc_final: 0.8148 (ttm) outliers start: 4 outliers final: 1 residues processed: 39 average time/residue: 1.3286 time to fit residues: 53.2772 Evaluate side-chains 34 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.083210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.058870 restraints weight = 7962.245| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.44 r_work: 0.2836 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3073 Z= 0.174 Angle : 0.522 6.529 4159 Z= 0.282 Chirality : 0.041 0.146 471 Planarity : 0.003 0.030 494 Dihedral : 5.648 33.833 426 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.24 % Allowed : 13.62 % Favored : 85.14 % 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: 3.09 (0.46), residues: 351 helix: 2.97 (0.32), residues: 252 sheet: 1.85 (1.18), residues: 22 loop : -1.29 (0.71), residues: 77 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 0.011 0.001 PHE B 31 TYR 0.007 0.001 TYR A 158 ARG 0.011 0.001 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.344 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 1.3969 time to fit residues: 58.8176 Evaluate side-chains 36 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 20 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 22 optimal weight: 0.1980 chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.083442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.058967 restraints weight = 7982.251| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.44 r_work: 0.2837 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3073 Z= 0.178 Angle : 0.541 8.858 4159 Z= 0.288 Chirality : 0.040 0.148 471 Planarity : 0.004 0.032 494 Dihedral : 5.254 30.181 426 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.93 % Allowed : 15.17 % Favored : 83.90 % 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: 3.20 (0.46), residues: 351 helix: 3.05 (0.32), residues: 252 sheet: 1.95 (1.19), residues: 22 loop : -1.28 (0.72), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 133 HIS 0.005 0.001 HIS A 100 PHE 0.011 0.001 PHE B 31 TYR 0.007 0.001 TYR B 68 ARG 0.010 0.001 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 216 ARG cc_start: 0.8470 (ttp80) cc_final: 0.8171 (ttp80) outliers start: 3 outliers final: 2 residues processed: 38 average time/residue: 1.2747 time to fit residues: 49.9459 Evaluate side-chains 34 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.0060 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.084325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.059976 restraints weight = 8030.567| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.43 r_work: 0.2863 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3073 Z= 0.154 Angle : 0.508 8.027 4159 Z= 0.271 Chirality : 0.040 0.144 471 Planarity : 0.003 0.030 494 Dihedral : 4.709 22.562 426 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.24 % Allowed : 16.10 % Favored : 82.66 % 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: 3.32 (0.46), residues: 351 helix: 3.15 (0.32), residues: 252 sheet: 2.03 (1.19), residues: 22 loop : -1.29 (0.71), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 133 HIS 0.003 0.001 HIS B 16 PHE 0.010 0.001 PHE B 31 TYR 0.007 0.001 TYR B 65 ARG 0.005 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 216 ARG cc_start: 0.8360 (ttp80) cc_final: 0.8102 (ttp80) REVERT: B 154 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.7983 (m-80) REVERT: B 209 GLU cc_start: 0.9197 (tp30) cc_final: 0.8859 (tp30) outliers start: 4 outliers final: 2 residues processed: 39 average time/residue: 1.2560 time to fit residues: 50.4395 Evaluate side-chains 34 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 0.0070 chunk 28 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.085112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.060874 restraints weight = 7977.117| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.47 r_work: 0.2881 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3073 Z= 0.140 Angle : 0.516 7.696 4159 Z= 0.276 Chirality : 0.039 0.141 471 Planarity : 0.004 0.050 494 Dihedral : 4.420 18.760 426 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.24 % Allowed : 16.10 % Favored : 82.66 % 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: 3.35 (0.46), residues: 351 helix: 3.15 (0.31), residues: 252 sheet: 2.21 (1.22), residues: 22 loop : -1.25 (0.70), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 133 HIS 0.002 0.001 HIS A 73 PHE 0.010 0.001 PHE B 31 TYR 0.015 0.001 TYR A 152 ARG 0.005 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.321 Fit side-chains REVERT: A 41 LYS cc_start: 0.8839 (ttpt) cc_final: 0.8300 (tmmt) REVERT: B 209 GLU cc_start: 0.9187 (tp30) cc_final: 0.8868 (tp30) outliers start: 4 outliers final: 2 residues processed: 39 average time/residue: 1.3294 time to fit residues: 53.3008 Evaluate side-chains 33 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.084971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.060512 restraints weight = 8029.382| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.44 r_work: 0.2874 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3073 Z= 0.157 Angle : 0.530 7.380 4159 Z= 0.284 Chirality : 0.039 0.141 471 Planarity : 0.005 0.073 494 Dihedral : 4.342 18.414 426 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.93 % Allowed : 17.96 % Favored : 81.11 % 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: 3.37 (0.46), residues: 351 helix: 3.17 (0.31), residues: 252 sheet: 2.21 (1.21), residues: 22 loop : -1.23 (0.71), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 133 HIS 0.002 0.001 HIS A 73 PHE 0.013 0.001 PHE B 31 TYR 0.007 0.001 TYR B 65 ARG 0.016 0.001 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.363 Fit side-chains REVERT: A 41 LYS cc_start: 0.8847 (ttpt) cc_final: 0.8255 (tmmt) REVERT: B 154 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.8054 (OUTLIER) REVERT: B 209 GLU cc_start: 0.9169 (tp30) cc_final: 0.8870 (tp30) outliers start: 3 outliers final: 3 residues processed: 34 average time/residue: 1.4813 time to fit residues: 51.8099 Evaluate side-chains 34 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.085263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.060747 restraints weight = 8094.953| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.44 r_work: 0.2888 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3073 Z= 0.149 Angle : 0.516 7.183 4159 Z= 0.279 Chirality : 0.039 0.141 471 Planarity : 0.004 0.058 494 Dihedral : 4.176 17.322 426 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.93 % Allowed : 18.27 % Favored : 80.80 % 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: 3.40 (0.46), residues: 351 helix: 3.20 (0.31), residues: 252 sheet: 2.22 (1.21), residues: 22 loop : -1.26 (0.71), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 133 HIS 0.002 0.000 HIS A 73 PHE 0.010 0.001 PHE B 31 TYR 0.014 0.001 TYR A 152 ARG 0.003 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.352 Fit side-chains REVERT: A 41 LYS cc_start: 0.8852 (ttpt) cc_final: 0.8257 (tmmt) REVERT: B 209 GLU cc_start: 0.9160 (tp30) cc_final: 0.8880 (tp30) outliers start: 3 outliers final: 2 residues processed: 35 average time/residue: 1.5080 time to fit residues: 54.2032 Evaluate side-chains 32 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 26 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.084626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.060214 restraints weight = 7781.800| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.38 r_work: 0.2869 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3073 Z= 0.181 Angle : 0.574 8.507 4159 Z= 0.304 Chirality : 0.040 0.140 471 Planarity : 0.004 0.058 494 Dihedral : 4.194 17.508 426 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.93 % Allowed : 18.27 % Favored : 80.80 % 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: 3.42 (0.46), residues: 351 helix: 3.21 (0.31), residues: 252 sheet: 2.21 (1.20), residues: 22 loop : -1.24 (0.70), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 133 HIS 0.002 0.001 HIS A 73 PHE 0.012 0.001 PHE B 31 TYR 0.007 0.001 TYR B 68 ARG 0.021 0.001 ARG A 216 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.298 Fit side-chains REVERT: A 41 LYS cc_start: 0.8841 (ttpt) cc_final: 0.8250 (tmmt) REVERT: B 209 GLU cc_start: 0.9154 (tp30) cc_final: 0.8875 (tp30) outliers start: 3 outliers final: 2 residues processed: 34 average time/residue: 1.4248 time to fit residues: 49.8249 Evaluate side-chains 32 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 20 optimal weight: 0.0170 chunk 12 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.085363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.061077 restraints weight = 7922.376| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.40 r_work: 0.2887 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3073 Z= 0.157 Angle : 0.568 7.720 4159 Z= 0.298 Chirality : 0.039 0.141 471 Planarity : 0.005 0.069 494 Dihedral : 4.087 15.674 426 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.93 % Allowed : 18.89 % Favored : 80.19 % 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: 3.43 (0.45), residues: 351 helix: 3.25 (0.31), residues: 252 sheet: 2.24 (1.21), residues: 22 loop : -1.35 (0.68), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 133 HIS 0.002 0.000 HIS A 73 PHE 0.011 0.001 PHE B 31 TYR 0.017 0.001 TYR A 152 ARG 0.028 0.001 ARG A 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2779.06 seconds wall clock time: 49 minutes 47.07 seconds (2987.07 seconds total)