Starting phenix.real_space_refine on Sat Nov 16 01:17:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qki_18463/11_2024/8qki_18463_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qki_18463/11_2024/8qki_18463.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qki_18463/11_2024/8qki_18463.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qki_18463/11_2024/8qki_18463.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qki_18463/11_2024/8qki_18463_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qki_18463/11_2024/8qki_18463_neut.cif" } resolution = 3.46 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= 0.000 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 90 5.16 5 C 6780 2.51 5 N 1680 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10188 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1670 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 4.48, per 1000 atoms: 0.44 Number of scatterers: 10188 At special positions: 0 Unit cell: (98.15, 101.4, 91.65, 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 90 16.00 O 1638 8.00 N 1680 7.00 C 6780 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 168 " 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: 2.83 Conformation dependent library (CDL) restraints added in 1.3 seconds 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2388 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 75.8% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 23 through 42 Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 108 Proline residue: A 87 - end of helix removed outlier: 3.760A pdb=" N ARG A 107 " --> pdb=" O LYS A 103 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 157 Processing helix chain 'A' and resid 183 through 220 Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 23 through 42 Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 108 Proline residue: B 87 - end of helix removed outlier: 3.760A pdb=" N ARG B 107 " --> pdb=" O LYS B 103 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 157 Processing helix chain 'B' and resid 183 through 220 Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 23 through 42 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 72 through 108 Proline residue: C 87 - end of helix removed outlier: 3.760A pdb=" N ARG C 107 " --> pdb=" O LYS C 103 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 108 " --> pdb=" O LYS C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 157 Processing helix chain 'C' and resid 183 through 220 Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 23 through 42 Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 72 through 108 Proline residue: D 87 - end of helix removed outlier: 3.761A pdb=" N ARG D 107 " --> pdb=" O LYS D 103 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D 108 " --> pdb=" O LYS D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 157 Processing helix chain 'D' and resid 183 through 220 Processing helix chain 'E' and resid 2 through 11 Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 23 through 42 Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 72 through 108 Proline residue: E 87 - end of helix removed outlier: 3.760A pdb=" N ARG E 107 " --> pdb=" O LYS E 103 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU E 108 " --> pdb=" O LYS E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 157 Processing helix chain 'E' and resid 183 through 220 Processing helix chain 'F' and resid 2 through 11 Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 23 through 42 Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 72 through 108 Proline residue: F 87 - end of helix removed outlier: 3.760A pdb=" N ARG F 107 " --> pdb=" O LYS F 103 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU F 108 " --> pdb=" O LYS F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 157 Processing helix chain 'F' and resid 183 through 220 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 Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53 Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53 Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53 Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53 780 hydrogen bonds defined for protein. 2304 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: 2.86 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3030 1.35 - 1.46: 2697 1.46 - 1.58: 4615 1.58 - 1.70: 2 1.70 - 1.82: 132 Bond restraints: 10476 Sorted by residual: bond pdb=" C6 CLR E 501 " pdb=" C7 CLR E 501 " ideal model delta sigma weight residual 1.492 1.542 -0.050 2.00e-02 2.50e+03 6.29e+00 bond pdb=" C6 CLR D 501 " pdb=" C7 CLR D 501 " ideal model delta sigma weight residual 1.492 1.542 -0.050 2.00e-02 2.50e+03 6.28e+00 bond pdb=" C6 CLR F 501 " pdb=" C7 CLR F 501 " ideal model delta sigma weight residual 1.492 1.542 -0.050 2.00e-02 2.50e+03 6.25e+00 bond pdb=" C6 CLR A 501 " pdb=" C7 CLR A 501 " ideal model delta sigma weight residual 1.492 1.542 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C6 CLR B 501 " pdb=" C7 CLR B 501 " ideal model delta sigma weight residual 1.492 1.541 -0.049 2.00e-02 2.50e+03 6.12e+00 ... (remaining 10471 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 13804 1.66 - 3.31: 332 3.31 - 4.97: 106 4.97 - 6.63: 44 6.63 - 8.28: 18 Bond angle restraints: 14304 Sorted by residual: angle pdb=" CB GLN A 98 " pdb=" CG GLN A 98 " pdb=" CD GLN A 98 " ideal model delta sigma weight residual 112.60 117.32 -4.72 1.70e+00 3.46e-01 7.72e+00 angle pdb=" CB GLN D 98 " pdb=" CG GLN D 98 " pdb=" CD GLN D 98 " ideal model delta sigma weight residual 112.60 117.31 -4.71 1.70e+00 3.46e-01 7.67e+00 angle pdb=" CB GLN C 98 " pdb=" CG GLN C 98 " pdb=" CD GLN C 98 " ideal model delta sigma weight residual 112.60 117.30 -4.70 1.70e+00 3.46e-01 7.64e+00 angle pdb=" C22 CLR C 501 " pdb=" C23 CLR C 501 " pdb=" C24 CLR C 501 " ideal model delta sigma weight residual 111.95 103.67 8.28 3.00e+00 1.11e-01 7.63e+00 angle pdb=" CB GLN E 98 " pdb=" CG GLN E 98 " pdb=" CD GLN E 98 " ideal model delta sigma weight residual 112.60 117.28 -4.68 1.70e+00 3.46e-01 7.57e+00 ... (remaining 14299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.70: 5473 11.70 - 23.40: 545 23.40 - 35.11: 240 35.11 - 46.81: 81 46.81 - 58.51: 36 Dihedral angle restraints: 6375 sinusoidal: 2703 harmonic: 3672 Sorted by residual: dihedral pdb=" CA ASP B 46 " pdb=" C ASP B 46 " pdb=" N GLU B 47 " pdb=" CA GLU B 47 " ideal model delta harmonic sigma weight residual 180.00 163.87 16.13 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA ASP F 46 " pdb=" C ASP F 46 " pdb=" N GLU F 47 " pdb=" CA GLU F 47 " ideal model delta harmonic sigma weight residual 180.00 163.89 16.11 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA ASP A 46 " pdb=" C ASP A 46 " pdb=" N GLU A 47 " pdb=" CA GLU A 47 " ideal model delta harmonic sigma weight residual 180.00 163.89 16.11 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 6372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1583 0.073 - 0.147: 97 0.147 - 0.220: 0 0.220 - 0.293: 7 0.293 - 0.367: 17 Chirality restraints: 1704 Sorted by residual: chirality pdb=" C17 CLR B 501 " pdb=" C13 CLR B 501 " pdb=" C16 CLR B 501 " pdb=" C20 CLR B 501 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" C17 CLR D 501 " pdb=" C13 CLR D 501 " pdb=" C16 CLR D 501 " pdb=" C20 CLR D 501 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" C17 CLR E 501 " pdb=" C13 CLR E 501 " pdb=" C16 CLR E 501 " pdb=" C20 CLR E 501 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 1701 not shown) Planarity restraints: 1674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 211 " -0.005 2.00e-02 2.50e+03 7.56e-03 1.14e+00 pdb=" CG TYR B 211 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 211 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 211 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 211 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 211 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 211 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 211 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 211 " -0.004 2.00e-02 2.50e+03 7.51e-03 1.13e+00 pdb=" CG TYR A 211 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 211 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 211 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 211 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 211 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 211 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 211 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 211 " 0.004 2.00e-02 2.50e+03 7.51e-03 1.13e+00 pdb=" CG TYR E 211 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR E 211 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR E 211 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR E 211 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 211 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR E 211 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 211 " -0.001 2.00e-02 2.50e+03 ... (remaining 1671 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 53 2.60 - 3.18: 8922 3.18 - 3.75: 17051 3.75 - 4.33: 21042 4.33 - 4.90: 36036 Nonbonded interactions: 83104 Sorted by model distance: nonbonded pdb=" SG CYS C 64 " pdb=" SG CYS C 168 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS B 60 " pdb=" SG CYS B 173 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS B 64 " pdb=" SG CYS B 168 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS F 64 " pdb=" SG CYS F 168 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS E 60 " pdb=" SG CYS E 173 " model vdw 2.031 3.760 ... (remaining 83099 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.090 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 : 0.004 0.050 10476 Z= 0.238 Angle : 0.752 8.284 14304 Z= 0.354 Chirality : 0.052 0.367 1704 Planarity : 0.002 0.014 1674 Dihedral : 12.595 58.509 3978 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.54 % Allowed : 3.76 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.14 (0.24), residues: 1218 helix: 2.50 (0.16), residues: 882 sheet: -0.88 (0.47), residues: 102 loop : -1.88 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 132 HIS 0.005 0.001 HIS F 94 PHE 0.006 0.001 PHE B 149 TYR 0.018 0.002 TYR B 211 ARG 0.003 0.000 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 314 time to evaluate : 1.274 Fit side-chains REVERT: A 13 VAL cc_start: 0.9149 (m) cc_final: 0.8898 (p) REVERT: A 34 MET cc_start: 0.7579 (mmm) cc_final: 0.7370 (mmt) REVERT: B 66 ASP cc_start: 0.7978 (t0) cc_final: 0.7717 (t0) REVERT: B 150 MET cc_start: 0.7869 (mmp) cc_final: 0.6999 (tmm) REVERT: C 34 MET cc_start: 0.7996 (mmm) cc_final: 0.7641 (mmt) REVERT: C 54 ASN cc_start: 0.8937 (t0) cc_final: 0.8634 (t0) REVERT: C 66 ASP cc_start: 0.7819 (t0) cc_final: 0.7543 (t0) REVERT: C 150 MET cc_start: 0.7649 (mmp) cc_final: 0.6819 (tmm) REVERT: D 54 ASN cc_start: 0.8893 (t0) cc_final: 0.8609 (t0) REVERT: D 66 ASP cc_start: 0.7719 (t0) cc_final: 0.7501 (t0) REVERT: D 150 MET cc_start: 0.7655 (mmp) cc_final: 0.6816 (tmm) REVERT: E 54 ASN cc_start: 0.8943 (t0) cc_final: 0.8601 (t0) REVERT: E 66 ASP cc_start: 0.7866 (t0) cc_final: 0.7598 (t0) REVERT: E 150 MET cc_start: 0.7793 (mmp) cc_final: 0.6954 (tmm) REVERT: F 34 MET cc_start: 0.8005 (mmm) cc_final: 0.7698 (mmt) REVERT: F 54 ASN cc_start: 0.8975 (t0) cc_final: 0.8654 (t0) REVERT: F 66 ASP cc_start: 0.7668 (t0) cc_final: 0.7443 (t0) REVERT: F 150 MET cc_start: 0.7706 (mmp) cc_final: 0.6814 (tmm) outliers start: 6 outliers final: 0 residues processed: 315 average time/residue: 0.2169 time to fit residues: 96.4603 Evaluate side-chains 259 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.7980 chunk 90 optimal weight: 0.0980 chunk 50 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10476 Z= 0.167 Angle : 0.562 6.057 14304 Z= 0.280 Chirality : 0.037 0.123 1704 Planarity : 0.003 0.017 1674 Dihedral : 5.014 53.612 1746 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.79 % Allowed : 12.72 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.13 (0.24), residues: 1218 helix: 3.21 (0.16), residues: 894 sheet: -0.65 (0.47), residues: 102 loop : -1.66 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 24 HIS 0.002 0.001 HIS F 97 PHE 0.007 0.001 PHE F 31 TYR 0.013 0.001 TYR A 157 ARG 0.002 0.000 ARG D 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 249 time to evaluate : 1.139 Fit side-chains REVERT: B 98 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7932 (mm-40) REVERT: B 150 MET cc_start: 0.8048 (mmp) cc_final: 0.7190 (tmm) REVERT: B 178 ASP cc_start: 0.7755 (p0) cc_final: 0.7452 (p0) REVERT: C 34 MET cc_start: 0.8009 (mmm) cc_final: 0.7629 (mmt) REVERT: C 54 ASN cc_start: 0.8837 (t0) cc_final: 0.8511 (t0) REVERT: C 66 ASP cc_start: 0.8041 (t0) cc_final: 0.7830 (t0) REVERT: C 144 LEU cc_start: 0.8643 (mm) cc_final: 0.8359 (mm) REVERT: C 150 MET cc_start: 0.7993 (mmp) cc_final: 0.7201 (tmm) REVERT: D 54 ASN cc_start: 0.8804 (t0) cc_final: 0.8444 (t0) REVERT: D 98 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7824 (mm-40) REVERT: D 144 LEU cc_start: 0.8622 (mm) cc_final: 0.8322 (mm) REVERT: D 150 MET cc_start: 0.7957 (mmp) cc_final: 0.7185 (tmm) REVERT: E 54 ASN cc_start: 0.8848 (t0) cc_final: 0.8492 (t0) REVERT: E 98 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7886 (mm-40) REVERT: E 150 MET cc_start: 0.8023 (mmp) cc_final: 0.7181 (tmm) REVERT: F 34 MET cc_start: 0.8037 (mmm) cc_final: 0.7695 (mmt) REVERT: F 54 ASN cc_start: 0.8896 (t0) cc_final: 0.8587 (t0) REVERT: F 89 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9147 (tp) REVERT: F 144 LEU cc_start: 0.8633 (mm) cc_final: 0.8341 (mm) REVERT: F 150 MET cc_start: 0.8019 (mmp) cc_final: 0.7199 (tmm) outliers start: 20 outliers final: 14 residues processed: 257 average time/residue: 0.2330 time to fit residues: 83.0168 Evaluate side-chains 238 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 223 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 126 HIS Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 178 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10476 Z= 0.230 Angle : 0.573 9.667 14304 Z= 0.285 Chirality : 0.039 0.153 1704 Planarity : 0.003 0.023 1674 Dihedral : 5.470 59.897 1746 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.42 % Allowed : 14.07 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.24), residues: 1218 helix: 3.30 (0.16), residues: 882 sheet: -0.36 (0.51), residues: 102 loop : -1.33 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 44 HIS 0.003 0.001 HIS C 16 PHE 0.011 0.001 PHE E 68 TYR 0.009 0.001 TYR F 7 ARG 0.003 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 1.231 Fit side-chains REVERT: A 123 HIS cc_start: 0.7846 (t70) cc_final: 0.7642 (t70) REVERT: B 144 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8828 (mm) REVERT: B 178 ASP cc_start: 0.8169 (p0) cc_final: 0.7955 (p0) REVERT: C 54 ASN cc_start: 0.8976 (t0) cc_final: 0.8705 (t0) REVERT: C 102 GLU cc_start: 0.8004 (tp30) cc_final: 0.7692 (mm-30) REVERT: C 144 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8858 (mm) REVERT: C 162 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.8086 (ttm) REVERT: D 102 GLU cc_start: 0.7960 (tp30) cc_final: 0.7616 (mm-30) REVERT: E 144 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8845 (mm) REVERT: F 54 ASN cc_start: 0.9000 (t0) cc_final: 0.8645 (t0) REVERT: F 102 GLU cc_start: 0.7983 (tp30) cc_final: 0.7674 (mm-30) REVERT: F 144 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8871 (mm) REVERT: F 162 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.8101 (ttm) outliers start: 27 outliers final: 14 residues processed: 228 average time/residue: 0.2305 time to fit residues: 73.2166 Evaluate side-chains 210 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 190 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 178 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN B 123 HIS ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN E 123 HIS F 67 GLN ** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10476 Z= 0.174 Angle : 0.533 7.741 14304 Z= 0.264 Chirality : 0.038 0.150 1704 Planarity : 0.002 0.020 1674 Dihedral : 5.246 57.869 1746 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.05 % Allowed : 13.62 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.41 (0.24), residues: 1218 helix: 3.38 (0.16), residues: 882 sheet: -0.31 (0.52), residues: 102 loop : -1.26 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 44 HIS 0.003 0.001 HIS F 123 PHE 0.007 0.001 PHE F 31 TYR 0.008 0.001 TYR A 65 ARG 0.002 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 1.176 Fit side-chains REVERT: A 150 MET cc_start: 0.7902 (mmm) cc_final: 0.7633 (tpp) REVERT: B 102 GLU cc_start: 0.8097 (tp30) cc_final: 0.7850 (mm-30) REVERT: B 144 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8882 (mm) REVERT: C 102 GLU cc_start: 0.7997 (tp30) cc_final: 0.7722 (mm-30) REVERT: C 144 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8862 (mm) REVERT: D 66 ASP cc_start: 0.8054 (t0) cc_final: 0.7833 (t0) REVERT: D 102 GLU cc_start: 0.7977 (tp30) cc_final: 0.7627 (mm-30) REVERT: D 144 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8873 (mm) REVERT: E 144 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8859 (mm) REVERT: F 102 GLU cc_start: 0.7989 (tp30) cc_final: 0.7675 (mm-30) REVERT: F 144 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8859 (mm) outliers start: 34 outliers final: 14 residues processed: 239 average time/residue: 0.2301 time to fit residues: 76.7389 Evaluate side-chains 216 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 144 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 98 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN C 94 HIS ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10476 Z= 0.187 Angle : 0.573 7.093 14304 Z= 0.289 Chirality : 0.039 0.146 1704 Planarity : 0.003 0.020 1674 Dihedral : 5.319 58.761 1746 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.24 % Allowed : 14.78 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.61 (0.24), residues: 1218 helix: 3.41 (0.16), residues: 894 sheet: -0.37 (0.52), residues: 102 loop : -0.83 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 44 HIS 0.008 0.001 HIS B 123 PHE 0.007 0.001 PHE A 31 TYR 0.008 0.001 TYR D 65 ARG 0.004 0.000 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: B 144 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8882 (mm) REVERT: C 102 GLU cc_start: 0.8009 (tp30) cc_final: 0.7720 (mm-30) REVERT: C 144 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8884 (mm) REVERT: D 102 GLU cc_start: 0.8002 (tp30) cc_final: 0.7606 (mm-30) REVERT: D 144 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8900 (mm) REVERT: E 144 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8883 (mm) REVERT: F 102 GLU cc_start: 0.7990 (tp30) cc_final: 0.7689 (mm-30) REVERT: F 144 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8891 (mm) outliers start: 25 outliers final: 15 residues processed: 236 average time/residue: 0.2497 time to fit residues: 80.4414 Evaluate side-chains 213 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 178 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 28 optimal weight: 0.4980 chunk 116 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 98 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS C 98 GLN ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 HIS F 98 GLN ** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10476 Z= 0.215 Angle : 0.586 7.492 14304 Z= 0.297 Chirality : 0.038 0.147 1704 Planarity : 0.003 0.019 1674 Dihedral : 5.394 56.905 1746 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.05 % Allowed : 15.86 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.45 (0.24), residues: 1218 helix: 3.34 (0.16), residues: 882 sheet: -0.39 (0.52), residues: 102 loop : -0.88 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 44 HIS 0.003 0.001 HIS E 126 PHE 0.008 0.001 PHE C 31 TYR 0.010 0.001 TYR F 65 ARG 0.003 0.000 ARG C 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 207 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: B 144 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8939 (mm) REVERT: C 66 ASP cc_start: 0.8095 (t0) cc_final: 0.7866 (t0) REVERT: C 102 GLU cc_start: 0.8066 (tp30) cc_final: 0.7788 (mm-30) REVERT: C 144 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8961 (mm) REVERT: D 41 GLU cc_start: 0.6691 (tt0) cc_final: 0.6490 (tt0) REVERT: D 98 GLN cc_start: 0.8411 (mp10) cc_final: 0.7984 (mp10) REVERT: D 102 GLU cc_start: 0.7982 (tp30) cc_final: 0.7657 (mm-30) REVERT: E 144 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8969 (mm) REVERT: F 102 GLU cc_start: 0.8031 (tp30) cc_final: 0.7731 (mm-30) REVERT: F 144 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8945 (mm) outliers start: 34 outliers final: 18 residues processed: 231 average time/residue: 0.2259 time to fit residues: 73.1338 Evaluate side-chains 219 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 178 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 115 optimal weight: 0.0670 chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 0.0870 chunk 53 optimal weight: 7.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 98 GLN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS B 98 GLN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS C 98 GLN ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 HIS ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 HIS F 98 GLN ** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10476 Z= 0.164 Angle : 0.596 8.361 14304 Z= 0.300 Chirality : 0.037 0.160 1704 Planarity : 0.003 0.021 1674 Dihedral : 5.132 53.724 1746 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.97 % Allowed : 16.04 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.48 (0.24), residues: 1218 helix: 3.39 (0.16), residues: 882 sheet: -0.41 (0.52), residues: 102 loop : -0.99 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 44 HIS 0.004 0.001 HIS A 123 PHE 0.007 0.001 PHE F 31 TYR 0.008 0.001 TYR F 171 ARG 0.003 0.000 ARG C 142 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 1.159 Fit side-chains REVERT: B 144 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8921 (mm) REVERT: C 102 GLU cc_start: 0.8014 (tp30) cc_final: 0.7751 (mm-30) REVERT: C 144 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8917 (mm) REVERT: C 194 MET cc_start: 0.8805 (mmp) cc_final: 0.8584 (mmt) REVERT: D 60 CYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8030 (t) REVERT: D 66 ASP cc_start: 0.8050 (t0) cc_final: 0.7816 (t0) REVERT: D 102 GLU cc_start: 0.7976 (tp30) cc_final: 0.7660 (mm-30) REVERT: D 173 CYS cc_start: 0.7664 (OUTLIER) cc_final: 0.6963 (m) REVERT: E 144 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8929 (mm) REVERT: F 66 ASP cc_start: 0.8033 (t0) cc_final: 0.7762 (t0) REVERT: F 102 GLU cc_start: 0.7997 (tp30) cc_final: 0.7720 (mm-30) REVERT: F 144 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8919 (mm) REVERT: F 194 MET cc_start: 0.8757 (mmp) cc_final: 0.8539 (mmt) outliers start: 22 outliers final: 12 residues processed: 223 average time/residue: 0.2266 time to fit residues: 71.1441 Evaluate side-chains 211 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 178 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 90 optimal weight: 0.0040 chunk 105 optimal weight: 0.6980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 98 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS B 98 GLN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS C 98 GLN ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 HIS E 98 GLN ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 HIS F 98 GLN ** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.5434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10476 Z= 0.160 Angle : 0.602 8.811 14304 Z= 0.302 Chirality : 0.037 0.155 1704 Planarity : 0.003 0.027 1674 Dihedral : 5.008 51.387 1746 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.51 % Allowed : 15.77 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.48 (0.24), residues: 1218 helix: 3.40 (0.16), residues: 882 sheet: -0.44 (0.51), residues: 102 loop : -1.02 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 44 HIS 0.003 0.001 HIS D 123 PHE 0.007 0.001 PHE A 31 TYR 0.012 0.001 TYR B 65 ARG 0.003 0.000 ARG F 183 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 1.209 Fit side-chains REVERT: B 65 TYR cc_start: 0.8467 (t80) cc_final: 0.8156 (t80) REVERT: B 144 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8873 (mm) REVERT: C 102 GLU cc_start: 0.7995 (tp30) cc_final: 0.7752 (mm-30) REVERT: C 144 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8926 (mm) REVERT: D 60 CYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7998 (t) REVERT: D 102 GLU cc_start: 0.7986 (tp30) cc_final: 0.7686 (mm-30) REVERT: D 173 CYS cc_start: 0.7589 (OUTLIER) cc_final: 0.6898 (m) REVERT: E 7 TYR cc_start: 0.8764 (t80) cc_final: 0.8478 (t80) REVERT: E 144 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8926 (mm) REVERT: F 66 ASP cc_start: 0.8002 (t0) cc_final: 0.7710 (t0) REVERT: F 102 GLU cc_start: 0.7994 (tp30) cc_final: 0.7718 (mm-30) REVERT: F 144 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.8930 (mm) REVERT: F 203 ILE cc_start: 0.9326 (pt) cc_final: 0.9118 (mt) outliers start: 28 outliers final: 17 residues processed: 228 average time/residue: 0.2252 time to fit residues: 72.2336 Evaluate side-chains 220 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 178 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 9.9990 chunk 101 optimal weight: 0.0470 chunk 107 optimal weight: 3.9990 chunk 64 optimal weight: 0.0470 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 98 GLN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS B 98 GLN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS C 98 GLN ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN E 94 HIS E 98 GLN ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 HIS F 98 GLN ** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10476 Z= 0.166 Angle : 0.620 10.043 14304 Z= 0.312 Chirality : 0.037 0.164 1704 Planarity : 0.003 0.026 1674 Dihedral : 4.996 51.640 1746 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.42 % Allowed : 16.85 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.48 (0.24), residues: 1218 helix: 3.41 (0.16), residues: 882 sheet: -0.41 (0.52), residues: 102 loop : -1.06 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 44 HIS 0.003 0.001 HIS D 123 PHE 0.007 0.001 PHE B 31 TYR 0.012 0.001 TYR F 151 ARG 0.003 0.000 ARG E 183 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 1.179 Fit side-chains REVERT: B 144 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8890 (mm) REVERT: C 7 TYR cc_start: 0.8827 (t80) cc_final: 0.8590 (t80) REVERT: C 102 GLU cc_start: 0.8002 (tp30) cc_final: 0.7756 (mm-30) REVERT: C 144 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8956 (mm) REVERT: D 60 CYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8014 (t) REVERT: D 102 GLU cc_start: 0.7984 (tp30) cc_final: 0.7687 (mm-30) REVERT: D 173 CYS cc_start: 0.7654 (OUTLIER) cc_final: 0.6961 (m) REVERT: E 7 TYR cc_start: 0.8757 (t80) cc_final: 0.8490 (t80) REVERT: E 144 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8936 (mm) REVERT: F 66 ASP cc_start: 0.8006 (t0) cc_final: 0.7723 (t0) REVERT: F 102 GLU cc_start: 0.7996 (tp30) cc_final: 0.7727 (mm-30) REVERT: F 144 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8926 (mm) outliers start: 27 outliers final: 16 residues processed: 224 average time/residue: 0.2385 time to fit residues: 75.0179 Evaluate side-chains 214 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 178 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.0970 chunk 79 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 98 GLN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS B 98 GLN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN C 94 HIS C 98 GLN ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 HIS ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 HIS E 98 GLN ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 HIS F 98 GLN ** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10476 Z= 0.167 Angle : 0.621 9.759 14304 Z= 0.311 Chirality : 0.037 0.170 1704 Planarity : 0.003 0.031 1674 Dihedral : 4.975 54.792 1746 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.24 % Allowed : 16.40 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.48 (0.24), residues: 1218 helix: 3.40 (0.16), residues: 882 sheet: -0.36 (0.52), residues: 102 loop : -1.08 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 44 HIS 0.003 0.001 HIS C 123 PHE 0.007 0.001 PHE A 31 TYR 0.027 0.001 TYR F 7 ARG 0.005 0.000 ARG C 183 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 1.168 Fit side-chains REVERT: B 46 ASP cc_start: 0.6890 (OUTLIER) cc_final: 0.6633 (t0) REVERT: B 66 ASP cc_start: 0.7997 (t0) cc_final: 0.7792 (t0) REVERT: B 144 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8874 (mm) REVERT: C 7 TYR cc_start: 0.8819 (t80) cc_final: 0.8615 (t80) REVERT: C 102 GLU cc_start: 0.8003 (tp30) cc_final: 0.7763 (mm-30) REVERT: C 144 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8925 (mm) REVERT: D 60 CYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8112 (t) REVERT: D 102 GLU cc_start: 0.7982 (tp30) cc_final: 0.7701 (mm-30) REVERT: D 173 CYS cc_start: 0.7462 (OUTLIER) cc_final: 0.6933 (m) REVERT: E 7 TYR cc_start: 0.8724 (t80) cc_final: 0.8509 (t80) REVERT: E 94 HIS cc_start: 0.7797 (t70) cc_final: 0.7581 (t-90) REVERT: E 144 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8905 (mm) REVERT: F 102 GLU cc_start: 0.8000 (tp30) cc_final: 0.7728 (mm-30) REVERT: F 144 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8925 (mm) outliers start: 25 outliers final: 16 residues processed: 223 average time/residue: 0.2187 time to fit residues: 68.8156 Evaluate side-chains 216 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 178 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 98 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS B 98 GLN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 HIS ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 GLN F 94 HIS ** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.066197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.057338 restraints weight = 31558.499| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.00 r_work: 0.2896 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10476 Z= 0.174 Angle : 0.616 9.850 14304 Z= 0.309 Chirality : 0.037 0.157 1704 Planarity : 0.003 0.026 1674 Dihedral : 5.018 55.009 1746 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.33 % Allowed : 17.20 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.54 (0.24), residues: 1218 helix: 3.39 (0.16), residues: 894 sheet: -0.37 (0.52), residues: 102 loop : -1.01 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 44 HIS 0.003 0.001 HIS E 126 PHE 0.007 0.001 PHE F 31 TYR 0.028 0.001 TYR F 7 ARG 0.004 0.000 ARG C 183 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2479.60 seconds wall clock time: 46 minutes 20.79 seconds (2780.79 seconds total)