Starting phenix.real_space_refine on Wed Jun 4 15:32:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qeu_13941/06_2025/7qeu_13941.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qeu_13941/06_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_13941/06_2025/7qeu_13941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qeu_13941/06_2025/7qeu_13941.map" model { file = "/net/cci-nas-00/data/ceres_data/7qeu_13941/06_2025/7qeu_13941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qeu_13941/06_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-5710/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: 3.96, per 1000 atoms: 1.32 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: 1.13 Conformation dependent library (CDL) restraints added in 400.1 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: 0.46 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: 1.13 Time building geometry restraints manager: 1.24 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.560 Find NCS groups from input model: 0.180 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: 0.010 Load rotamer database and sin/cos tables:22.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.630 ------------------------------------------------------------------------------- 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 3079 Z= 0.321 Angle : 0.799 7.832 4171 Z= 0.376 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 Details of bonding type rmsd hydrogen bonds : bond 0.26966 ( 215) hydrogen bonds : angle 6.83498 ( 627) SS BOND : bond 0.00238 ( 6) SS BOND : angle 1.18189 ( 12) covalent geometry : bond 0.00742 ( 3073) covalent geometry : angle 0.79809 ( 4159) *********************** 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 : 0.346 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 1.5225 time to fit residues: 56.1587 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 : 0.311 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.081921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.057540 restraints weight = 7934.781| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.37 r_work: 0.2808 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3079 Z= 0.160 Angle : 0.582 6.760 4171 Z= 0.323 Chirality : 0.043 0.139 471 Planarity : 0.004 0.031 494 Dihedral : 7.413 52.270 426 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.66 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 0.006 0.000 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.07153 ( 215) hydrogen bonds : angle 4.07435 ( 627) SS BOND : bond 0.00229 ( 6) SS BOND : angle 1.09963 ( 12) covalent geometry : bond 0.00328 ( 3073) covalent geometry : angle 0.57946 ( 4159) *********************** 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 : 0.314 Fit side-chains revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8297 (mm-30) REVERT: A 216 ARG cc_start: 0.8489 (ttp80) cc_final: 0.7950 (tmt170) REVERT: B 42 GLU cc_start: 0.6809 (pp20) cc_final: 0.6483 (pp20) outliers start: 4 outliers final: 1 residues processed: 41 average time/residue: 1.2585 time to fit residues: 53.0559 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 : 0.382 ------------------------------------------------------------------------------- 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: 3.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 31 optimal weight: 0.4980 chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.082034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.057577 restraints weight = 7796.484| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.41 r_work: 0.2796 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 3079 Z= 0.151 Angle : 0.539 6.445 4171 Z= 0.294 Chirality : 0.042 0.144 471 Planarity : 0.003 0.029 494 Dihedral : 6.419 41.789 426 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.55 % Allowed : 11.46 % Favored : 87.00 % 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: 2.95 (0.46), residues: 351 helix: 2.97 (0.32), residues: 245 sheet: 1.63 (1.14), residues: 22 loop : -1.27 (0.69), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 133 HIS 0.002 0.001 HIS A 73 PHE 0.010 0.001 PHE B 31 TYR 0.010 0.001 TYR B 158 ARG 0.005 0.000 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.06160 ( 215) hydrogen bonds : angle 3.81042 ( 627) SS BOND : bond 0.00168 ( 6) SS BOND : angle 0.93678 ( 12) covalent geometry : bond 0.00349 ( 3073) covalent geometry : angle 0.53739 ( 4159) *********************** 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 41 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: B 93 MET cc_start: 0.8422 (ttm) cc_final: 0.8148 (ttm) outliers start: 5 outliers final: 1 residues processed: 39 average time/residue: 1.2411 time to fit residues: 49.8459 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 : 0.319 ------------------------------------------------------------------------------- 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: 0.5980 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 4 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.083295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.058985 restraints weight = 7970.827| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.44 r_work: 0.2838 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3079 Z= 0.118 Angle : 0.520 6.814 4171 Z= 0.280 Chirality : 0.040 0.146 471 Planarity : 0.004 0.040 494 Dihedral : 5.590 33.587 426 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.24 % Allowed : 13.31 % Favored : 85.45 % 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: 3.08 (0.46), residues: 351 helix: 2.97 (0.32), residues: 252 sheet: 1.83 (1.17), residues: 22 loop : -1.31 (0.71), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 133 HIS 0.002 0.001 HIS B 16 PHE 0.010 0.001 PHE B 31 TYR 0.007 0.001 TYR A 158 ARG 0.007 0.000 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.04984 ( 215) hydrogen bonds : angle 3.49496 ( 627) SS BOND : bond 0.00152 ( 6) SS BOND : angle 0.82706 ( 12) covalent geometry : bond 0.00246 ( 3073) covalent geometry : angle 0.51856 ( 4159) *********************** 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 : 0.318 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 1.4094 time to fit residues: 59.3478 Evaluate side-chains 37 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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: 0.8980 chunk 8 optimal weight: 1.9990 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: 1.9990 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 = 0.3550 r_free = 0.3550 target = 0.083050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.058661 restraints weight = 7962.662| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.44 r_work: 0.2827 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3079 Z= 0.132 Angle : 0.545 8.651 4171 Z= 0.291 Chirality : 0.041 0.147 471 Planarity : 0.004 0.031 494 Dihedral : 5.323 30.887 426 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.93 % Allowed : 14.55 % Favored : 84.52 % 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: 3.17 (0.46), residues: 351 helix: 3.03 (0.32), residues: 252 sheet: 1.92 (1.18), residues: 22 loop : -1.27 (0.72), 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 100 PHE 0.012 0.001 PHE B 31 TYR 0.008 0.001 TYR B 68 ARG 0.010 0.001 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.04974 ( 215) hydrogen bonds : angle 3.43560 ( 627) SS BOND : bond 0.00150 ( 6) SS BOND : angle 0.80041 ( 12) covalent geometry : bond 0.00298 ( 3073) covalent geometry : angle 0.54426 ( 4159) *********************** 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 : 0.319 Fit side-chains revert: symmetry clash REVERT: A 216 ARG cc_start: 0.8471 (ttp80) cc_final: 0.8171 (ttp80) outliers start: 3 outliers final: 2 residues processed: 38 average time/residue: 1.2948 time to fit residues: 50.6250 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 : 0.318 ------------------------------------------------------------------------------- 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: 0.0370 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.084194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.059842 restraints weight = 8018.198| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.45 r_work: 0.2856 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3079 Z= 0.112 Angle : 0.512 8.024 4171 Z= 0.274 Chirality : 0.040 0.140 471 Planarity : 0.003 0.029 494 Dihedral : 4.809 23.948 426 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 : 0.93 % Allowed : 16.41 % 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: 3.26 (0.46), residues: 351 helix: 3.11 (0.32), residues: 252 sheet: 2.02 (1.19), residues: 22 loop : -1.30 (0.71), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 133 HIS 0.002 0.001 HIS A 73 PHE 0.010 0.001 PHE B 31 TYR 0.006 0.001 TYR B 65 ARG 0.006 0.000 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.04489 ( 215) hydrogen bonds : angle 3.31742 ( 627) SS BOND : bond 0.00146 ( 6) SS BOND : angle 0.77299 ( 12) covalent geometry : bond 0.00236 ( 3073) covalent geometry : angle 0.51144 ( 4159) *********************** 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: 3 poor density : 36 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 216 ARG cc_start: 0.8372 (ttp80) cc_final: 0.8120 (ttp80) REVERT: B 209 GLU cc_start: 0.9193 (tp30) cc_final: 0.8855 (tp30) outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 1.2337 time to fit residues: 49.6541 Evaluate side-chains 35 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 0.0170 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 18 optimal weight: 0.0170 chunk 33 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 13 optimal weight: 0.0170 chunk 3 optimal weight: 0.5980 overall best weight: 0.2694 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.086613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.062414 restraints weight = 7974.813| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.45 r_work: 0.2921 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3079 Z= 0.102 Angle : 0.494 7.646 4171 Z= 0.261 Chirality : 0.039 0.137 471 Planarity : 0.003 0.029 494 Dihedral : 4.133 17.861 426 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.24 % Allowed : 16.41 % Favored : 82.35 % 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: 3.29 (0.45), residues: 351 helix: 3.13 (0.31), residues: 252 sheet: 2.25 (1.22), residues: 22 loop : -1.36 (0.68), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 133 HIS 0.003 0.001 HIS A 73 PHE 0.011 0.001 PHE B 31 TYR 0.015 0.001 TYR A 152 ARG 0.006 0.000 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 215) hydrogen bonds : angle 3.14902 ( 627) SS BOND : bond 0.00131 ( 6) SS BOND : angle 0.73685 ( 12) covalent geometry : bond 0.00204 ( 3073) covalent geometry : angle 0.49266 ( 4159) *********************** 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 41 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.375 Fit side-chains REVERT: B 209 GLU cc_start: 0.9169 (tp30) cc_final: 0.8871 (tp30) outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 1.3473 time to fit residues: 56.7763 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 : 0.352 ------------------------------------------------------------------------------- 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: 10.0000 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.084873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.060420 restraints weight = 8005.974| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.43 r_work: 0.2875 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 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 : 0.003 0.031 3079 Z= 0.119 Angle : 0.532 7.357 4171 Z= 0.286 Chirality : 0.040 0.137 471 Planarity : 0.004 0.048 494 Dihedral : 4.170 17.463 426 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.24 % Allowed : 17.96 % 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: 3.44 (0.46), residues: 351 helix: 3.22 (0.31), residues: 252 sheet: 2.32 (1.21), residues: 22 loop : -1.25 (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 0.014 0.001 PHE B 31 TYR 0.009 0.001 TYR A 158 ARG 0.017 0.001 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.04164 ( 215) hydrogen bonds : angle 3.19355 ( 627) SS BOND : bond 0.00139 ( 6) SS BOND : angle 0.73998 ( 12) covalent geometry : bond 0.00262 ( 3073) covalent geometry : angle 0.53135 ( 4159) *********************** 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 36 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.567 Fit side-chains REVERT: A 41 LYS cc_start: 0.8841 (ttpt) cc_final: 0.8335 (tmmt) REVERT: B 209 GLU cc_start: 0.9162 (tp30) cc_final: 0.8881 (tp30) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 1.5788 time to fit residues: 58.6797 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 : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.085106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.060563 restraints weight = 8068.627| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.43 r_work: 0.2880 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3079 Z= 0.111 Angle : 0.526 7.213 4171 Z= 0.280 Chirality : 0.040 0.138 471 Planarity : 0.003 0.030 494 Dihedral : 4.099 17.277 426 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.93 % Allowed : 18.58 % Favored : 80.50 % 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: 3.46 (0.46), residues: 351 helix: 3.24 (0.31), residues: 252 sheet: 2.35 (1.22), residues: 22 loop : -1.26 (0.70), 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 0.013 0.001 PHE B 31 TYR 0.016 0.001 TYR A 152 ARG 0.003 0.000 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 215) hydrogen bonds : angle 3.16872 ( 627) SS BOND : bond 0.00138 ( 6) SS BOND : angle 0.72428 ( 12) covalent geometry : bond 0.00242 ( 3073) covalent geometry : angle 0.52521 ( 4159) *********************** 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 36 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.309 Fit side-chains REVERT: A 41 LYS cc_start: 0.8851 (ttpt) cc_final: 0.8362 (tmmt) REVERT: A 216 ARG cc_start: 0.8025 (ttp80) cc_final: 0.7811 (ttp80) REVERT: B 209 GLU cc_start: 0.9153 (tp30) cc_final: 0.8879 (tp30) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 1.4956 time to fit residues: 55.2766 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 : 0.317 ------------------------------------------------------------------------------- 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: 8.9990 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.0470 chunk 6 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.085590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.061227 restraints weight = 7728.085| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.37 r_work: 0.2897 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 3079 Z= 0.110 Angle : 0.525 7.102 4171 Z= 0.280 Chirality : 0.039 0.136 471 Planarity : 0.004 0.033 494 Dihedral : 3.943 15.558 426 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.62 % Allowed : 19.20 % 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: 3.47 (0.45), residues: 351 helix: 3.27 (0.31), residues: 252 sheet: 2.37 (1.22), residues: 22 loop : -1.35 (0.68), 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 0.005 0.001 TYR B 68 ARG 0.004 0.000 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 215) hydrogen bonds : angle 3.13988 ( 627) SS BOND : bond 0.00139 ( 6) SS BOND : angle 0.71526 ( 12) covalent geometry : bond 0.00237 ( 3073) covalent geometry : angle 0.52466 ( 4159) ********************** 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 35 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.421 Fit side-chains REVERT: A 41 LYS cc_start: 0.8841 (ttpt) cc_final: 0.8393 (tmtt) REVERT: B 209 GLU cc_start: 0.9117 (tp30) cc_final: 0.8839 (tp30) outliers start: 2 outliers final: 2 residues processed: 35 average time/residue: 1.3592 time to fit residues: 49.0523 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 : 0.354 ------------------------------------------------------------------------------- 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: 0.7980 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3564 r_free = 0.3564 target = 0.083991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.059585 restraints weight = 7887.818| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.41 r_work: 0.2852 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3079 Z= 0.136 Angle : 0.590 9.698 4171 Z= 0.306 Chirality : 0.041 0.191 471 Planarity : 0.005 0.068 494 Dihedral : 4.109 17.284 426 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.62 % Allowed : 19.20 % 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: 3.46 (0.45), residues: 351 helix: 3.24 (0.31), residues: 252 sheet: 2.29 (1.21), residues: 22 loop : -1.26 (0.70), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 133 HIS 0.001 0.000 HIS B 16 PHE 0.012 0.001 PHE B 31 TYR 0.017 0.001 TYR A 152 ARG 0.015 0.001 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.04326 ( 215) hydrogen bonds : angle 3.16726 ( 627) SS BOND : bond 0.00148 ( 6) SS BOND : angle 0.76044 ( 12) covalent geometry : bond 0.00316 ( 3073) covalent geometry : angle 0.58931 ( 4159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2809.06 seconds wall clock time: 48 minutes 39.13 seconds (2919.13 seconds total)