Starting phenix.real_space_refine on Fri Apr 5 18:19:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xgy_33189/04_2024/7xgy_33189_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xgy_33189/04_2024/7xgy_33189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xgy_33189/04_2024/7xgy_33189.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xgy_33189/04_2024/7xgy_33189.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xgy_33189/04_2024/7xgy_33189_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xgy_33189/04_2024/7xgy_33189_updated.pdb" } resolution = 3.5 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= 0.001 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: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 12 5.16 5 C 2954 2.51 5 N 780 2.21 5 O 805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 64": "OD1" <-> "OD2" Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "C PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 64": "OD1" <-> "OD2" Residue "C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 6": "OE1" <-> "OE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D ASP 99": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 4555 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1069 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "B" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1123 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "C" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1068 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1123 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.10, per 1000 atoms: 0.68 Number of scatterers: 4555 At special positions: 0 Unit cell: (78.3841, 77.3459, 66.9639, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 12 16.00 O 805 8.00 N 780 7.00 C 2954 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 838.5 milliseconds 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1068 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 0 sheets defined 73.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 4 through 35 removed outlier: 5.437A pdb=" N ALA A 19 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N HIS A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA A 21 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLY A 22 " --> pdb=" O GLY A 18 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLU A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 removed outlier: 3.920A pdb=" N THR A 41 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 71 Processing helix chain 'A' and resid 76 through 89 removed outlier: 5.417A pdb=" N ALA A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 112 Processing helix chain 'A' and resid 119 through 137 Processing helix chain 'B' and resid 5 through 16 Processing helix chain 'B' and resid 23 through 34 Processing helix chain 'B' and resid 38 through 40 No H-bonds generated for 'chain 'B' and resid 38 through 40' Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 58 through 76 Processing helix chain 'B' and resid 81 through 84 No H-bonds generated for 'chain 'B' and resid 81 through 84' Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 118 removed outlier: 3.871A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 141 Processing helix chain 'C' and resid 4 through 35 removed outlier: 5.437A pdb=" N ALA C 19 " --> pdb=" O GLY C 15 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N HIS C 20 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA C 21 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N GLY C 22 " --> pdb=" O GLY C 18 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLU C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 42 removed outlier: 3.921A pdb=" N THR C 41 " --> pdb=" O THR C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 71 Processing helix chain 'C' and resid 76 through 89 removed outlier: 5.417A pdb=" N ALA C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LEU C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 112 Processing helix chain 'C' and resid 119 through 137 Processing helix chain 'D' and resid 5 through 16 Processing helix chain 'D' and resid 23 through 34 Processing helix chain 'D' and resid 38 through 40 No H-bonds generated for 'chain 'D' and resid 38 through 40' Processing helix chain 'D' and resid 43 through 45 No H-bonds generated for 'chain 'D' and resid 43 through 45' Processing helix chain 'D' and resid 51 through 56 Processing helix chain 'D' and resid 58 through 76 Processing helix chain 'D' and resid 81 through 84 No H-bonds generated for 'chain 'D' and resid 81 through 84' Processing helix chain 'D' and resid 87 through 94 Processing helix chain 'D' and resid 100 through 118 removed outlier: 3.871A pdb=" N ARG D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 141 280 hydrogen bonds defined for protein. 828 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: 1.25 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.38: 1884 1.38 - 1.54: 2768 1.54 - 1.71: 13 1.71 - 1.87: 18 1.87 - 2.03: 16 Bond restraints: 4699 Sorted by residual: bond pdb=" C MET C 76 " pdb=" N PRO C 77 " ideal model delta sigma weight residual 1.336 1.354 -0.019 1.23e-02 6.61e+03 2.36e+00 bond pdb=" C MET A 76 " pdb=" N PRO A 77 " ideal model delta sigma weight residual 1.336 1.354 -0.019 1.23e-02 6.61e+03 2.36e+00 bond pdb=" CA MET C 76 " pdb=" C MET C 76 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.26e-02 6.30e+03 2.12e+00 bond pdb=" C1C HEM D 201 " pdb=" CHC HEM D 201 " ideal model delta sigma weight residual 1.378 1.349 0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" ND HEM B 201 " pdb="FE HEM B 201 " ideal model delta sigma weight residual 2.080 1.979 0.101 7.00e-02 2.04e+02 2.09e+00 ... (remaining 4694 not shown) Histogram of bond angle deviations from ideal: 86.58 - 102.68: 32 102.68 - 118.78: 3837 118.78 - 134.89: 2572 134.89 - 150.99: 0 150.99 - 167.10: 8 Bond angle restraints: 6449 Sorted by residual: angle pdb=" CA MET A 76 " pdb=" C MET A 76 " pdb=" N PRO A 77 " ideal model delta sigma weight residual 118.44 124.03 -5.59 1.59e+00 3.96e-01 1.24e+01 angle pdb=" CA MET C 76 " pdb=" C MET C 76 " pdb=" N PRO C 77 " ideal model delta sigma weight residual 118.44 124.01 -5.57 1.59e+00 3.96e-01 1.23e+01 angle pdb=" N MET A 76 " pdb=" CA MET A 76 " pdb=" C MET A 76 " ideal model delta sigma weight residual 109.81 116.31 -6.50 2.21e+00 2.05e-01 8.64e+00 angle pdb=" N MET C 76 " pdb=" CA MET C 76 " pdb=" C MET C 76 " ideal model delta sigma weight residual 109.81 116.29 -6.48 2.21e+00 2.05e-01 8.61e+00 angle pdb=" CA TYR D 145 " pdb=" CB TYR D 145 " pdb=" CG TYR D 145 " ideal model delta sigma weight residual 113.90 118.98 -5.08 1.80e+00 3.09e-01 7.95e+00 ... (remaining 6444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 2304 16.75 - 33.51: 267 33.51 - 50.26: 72 50.26 - 67.01: 16 67.01 - 83.77: 8 Dihedral angle restraints: 2667 sinusoidal: 1017 harmonic: 1650 Sorted by residual: dihedral pdb=" CA TYR D 145 " pdb=" C TYR D 145 " pdb=" N HIS D 146 " pdb=" CA HIS D 146 " ideal model delta harmonic sigma weight residual -180.00 -154.06 -25.94 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA TYR B 145 " pdb=" C TYR B 145 " pdb=" N HIS B 146 " pdb=" CA HIS B 146 " ideal model delta harmonic sigma weight residual 180.00 -154.10 -25.90 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA ASN D 19 " pdb=" C ASN D 19 " pdb=" N VAL D 20 " pdb=" CA VAL D 20 " ideal model delta harmonic sigma weight residual 180.00 -154.27 -25.73 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 2664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 442 0.046 - 0.092: 183 0.092 - 0.138: 55 0.138 - 0.184: 14 0.184 - 0.230: 6 Chirality restraints: 700 Sorted by residual: chirality pdb=" CA MET A 76 " pdb=" N MET A 76 " pdb=" C MET A 76 " pdb=" CB MET A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA MET C 76 " pdb=" N MET C 76 " pdb=" C MET C 76 " pdb=" CB MET C 76 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB VAL D 109 " pdb=" CA VAL D 109 " pdb=" CG1 VAL D 109 " pdb=" CG2 VAL D 109 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 697 not shown) Planarity restraints: 806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 124 " -0.065 5.00e-02 4.00e+02 9.69e-02 1.50e+01 pdb=" N PRO D 125 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO D 125 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 125 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 124 " 0.065 5.00e-02 4.00e+02 9.69e-02 1.50e+01 pdb=" N PRO B 125 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO B 125 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 125 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 123 " 0.049 5.00e-02 4.00e+02 7.47e-02 8.93e+00 pdb=" N PRO D 124 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 124 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 124 " 0.041 5.00e-02 4.00e+02 ... (remaining 803 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1400 2.83 - 3.34: 4500 3.34 - 3.86: 7991 3.86 - 4.38: 9268 4.38 - 4.90: 15036 Nonbonded interactions: 38195 Sorted by model distance: nonbonded pdb=" O ALA C 130 " pdb=" OG1 THR C 134 " model vdw 2.307 2.440 nonbonded pdb=" O ALA A 130 " pdb=" OG1 THR A 134 " model vdw 2.308 2.440 nonbonded pdb=" O PHE C 128 " pdb=" OG SER C 131 " model vdw 2.329 2.440 nonbonded pdb=" O PHE A 128 " pdb=" OG SER A 131 " model vdw 2.329 2.440 nonbonded pdb=" O ASP C 64 " pdb=" OG1 THR C 67 " model vdw 2.347 2.440 ... (remaining 38190 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 80 or (resid 81 through 82 and (name N or name C \ A or name C or name O or name CB )) or resid 83 through 141 or resid 201)) selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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 group one per residue 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: 1.900 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: 3.670 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 17.190 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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: 26.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 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 : 0.008 0.101 4699 Z= 0.563 Angle : 1.160 16.538 6449 Z= 0.541 Chirality : 0.058 0.230 700 Planarity : 0.010 0.097 806 Dihedral : 16.479 83.765 1599 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.17 % Allowed : 14.53 % Favored : 83.30 % 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: -3.05 (0.30), residues: 566 helix: -1.76 (0.20), residues: 452 sheet: None (None), residues: 0 loop : -2.20 (0.59), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 14 HIS 0.005 0.002 HIS C 20 PHE 0.022 0.003 PHE D 45 TYR 0.021 0.002 TYR B 145 ARG 0.001 0.000 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 192 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.6585 (t70) cc_final: 0.6374 (t0) REVERT: A 85 ASP cc_start: 0.6774 (t0) cc_final: 0.6539 (t70) REVERT: A 112 HIS cc_start: 0.7394 (m-70) cc_final: 0.6419 (m-70) REVERT: B 40 ARG cc_start: 0.6707 (tpt170) cc_final: 0.6256 (tpt170) REVERT: B 59 LYS cc_start: 0.7877 (mtpt) cc_final: 0.7537 (mtmt) REVERT: B 99 ASP cc_start: 0.6594 (t0) cc_final: 0.6117 (t70) REVERT: B 101 GLU cc_start: 0.8079 (pm20) cc_final: 0.7665 (pm20) REVERT: B 131 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7826 (tm-30) REVERT: C 6 ASP cc_start: 0.7273 (p0) cc_final: 0.6937 (p0) REVERT: C 85 ASP cc_start: 0.6877 (t0) cc_final: 0.6584 (t70) REVERT: C 112 HIS cc_start: 0.7375 (m-70) cc_final: 0.6230 (m90) REVERT: D 40 ARG cc_start: 0.6687 (tpt170) cc_final: 0.6370 (tpt170) REVERT: D 59 LYS cc_start: 0.7827 (mtpt) cc_final: 0.7495 (mtmt) REVERT: D 99 ASP cc_start: 0.6574 (t0) cc_final: 0.6221 (t70) REVERT: D 131 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7827 (tm-30) outliers start: 10 outliers final: 2 residues processed: 196 average time/residue: 0.2016 time to fit residues: 47.4505 Evaluate side-chains 151 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain C residue 38 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 0.1980 chunk 42 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 14 optimal weight: 0.4980 chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 HIS B 146 HIS D 143 HIS D 146 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4699 Z= 0.246 Angle : 0.692 9.750 6449 Z= 0.324 Chirality : 0.042 0.139 700 Planarity : 0.007 0.089 806 Dihedral : 10.034 75.603 632 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.69 % Allowed : 24.51 % Favored : 71.80 % 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: -0.69 (0.35), residues: 566 helix: -0.02 (0.24), residues: 446 sheet: None (None), residues: 0 loop : -1.69 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 37 HIS 0.010 0.001 HIS B 143 PHE 0.012 0.001 PHE B 85 TYR 0.012 0.001 TYR D 145 ARG 0.005 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6235 (tt0) cc_final: 0.5765 (tt0) REVERT: A 47 ASP cc_start: 0.6518 (t70) cc_final: 0.6270 (t0) REVERT: A 109 LEU cc_start: 0.9081 (mt) cc_final: 0.8876 (mt) REVERT: A 117 PHE cc_start: 0.6483 (OUTLIER) cc_final: 0.6031 (m-80) REVERT: B 30 ARG cc_start: 0.7924 (mtt-85) cc_final: 0.7649 (mtt90) REVERT: B 59 LYS cc_start: 0.7808 (mtpt) cc_final: 0.7375 (mtmt) REVERT: B 101 GLU cc_start: 0.7680 (pm20) cc_final: 0.6712 (pm20) REVERT: B 104 ARG cc_start: 0.7414 (ttm170) cc_final: 0.7120 (ttm-80) REVERT: C 6 ASP cc_start: 0.7320 (p0) cc_final: 0.6972 (p0) REVERT: C 27 GLU cc_start: 0.6274 (tt0) cc_final: 0.5553 (tt0) REVERT: C 112 HIS cc_start: 0.6880 (m-70) cc_final: 0.6182 (m90) REVERT: D 40 ARG cc_start: 0.6716 (tpt170) cc_final: 0.6334 (tpt170) REVERT: D 59 LYS cc_start: 0.7778 (mtpt) cc_final: 0.7430 (mtmt) REVERT: D 101 GLU cc_start: 0.7706 (pm20) cc_final: 0.7491 (pm20) REVERT: D 104 ARG cc_start: 0.7417 (ttm170) cc_final: 0.7175 (ttm-80) outliers start: 17 outliers final: 13 residues processed: 176 average time/residue: 0.1977 time to fit residues: 41.8523 Evaluate side-chains 176 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 84 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN C 58 HIS ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4699 Z= 0.278 Angle : 0.702 9.623 6449 Z= 0.329 Chirality : 0.044 0.220 700 Planarity : 0.007 0.085 806 Dihedral : 9.979 74.006 632 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.56 % Allowed : 26.46 % Favored : 68.98 % 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: 0.30 (0.36), residues: 566 helix: 0.64 (0.25), residues: 444 sheet: None (None), residues: 0 loop : -1.17 (0.63), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 37 HIS 0.006 0.001 HIS A 122 PHE 0.010 0.001 PHE A 36 TYR 0.011 0.001 TYR D 145 ARG 0.003 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 167 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6121 (tt0) cc_final: 0.5671 (tt0) REVERT: A 47 ASP cc_start: 0.6505 (t70) cc_final: 0.6263 (t0) REVERT: B 59 LYS cc_start: 0.7790 (mtpt) cc_final: 0.7541 (mtmt) REVERT: C 6 ASP cc_start: 0.7344 (p0) cc_final: 0.7037 (p0) REVERT: C 27 GLU cc_start: 0.6296 (tt0) cc_final: 0.5572 (tt0) REVERT: C 85 ASP cc_start: 0.7037 (t70) cc_final: 0.6829 (t70) REVERT: C 112 HIS cc_start: 0.6955 (m-70) cc_final: 0.6286 (m90) REVERT: D 30 ARG cc_start: 0.8084 (mtt-85) cc_final: 0.7861 (mtt90) REVERT: D 40 ARG cc_start: 0.6789 (tpt170) cc_final: 0.6465 (tpt170) REVERT: D 59 LYS cc_start: 0.7811 (mtpt) cc_final: 0.7480 (mtmt) REVERT: D 101 GLU cc_start: 0.7838 (pm20) cc_final: 0.7487 (pm20) REVERT: D 104 ARG cc_start: 0.7593 (ttm170) cc_final: 0.7382 (ttm-80) outliers start: 21 outliers final: 20 residues processed: 175 average time/residue: 0.1763 time to fit residues: 37.7872 Evaluate side-chains 181 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 161 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 20 HIS Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 84 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.4980 chunk 5 optimal weight: 8.9990 chunk 24 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 HIS ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4699 Z= 0.228 Angle : 0.674 8.884 6449 Z= 0.319 Chirality : 0.044 0.234 700 Planarity : 0.007 0.081 806 Dihedral : 9.470 71.157 632 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.64 % Allowed : 26.46 % Favored : 67.90 % 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: 0.77 (0.36), residues: 566 helix: 0.99 (0.25), residues: 442 sheet: None (None), residues: 0 loop : -1.01 (0.63), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 37 HIS 0.006 0.001 HIS A 122 PHE 0.009 0.001 PHE B 85 TYR 0.009 0.001 TYR D 145 ARG 0.002 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 174 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6102 (tt0) cc_final: 0.5669 (tt0) REVERT: A 47 ASP cc_start: 0.6498 (t70) cc_final: 0.6265 (t0) REVERT: B 59 LYS cc_start: 0.7817 (mtpt) cc_final: 0.7538 (mtmt) REVERT: B 99 ASP cc_start: 0.7361 (t70) cc_final: 0.6165 (t70) REVERT: B 104 ARG cc_start: 0.7417 (ttm170) cc_final: 0.7194 (ttm-80) REVERT: C 6 ASP cc_start: 0.7265 (p0) cc_final: 0.6958 (p0) REVERT: C 27 GLU cc_start: 0.6233 (tt0) cc_final: 0.5675 (tt0) REVERT: C 112 HIS cc_start: 0.6928 (m-70) cc_final: 0.6393 (m90) REVERT: D 30 ARG cc_start: 0.8010 (mtt-85) cc_final: 0.7800 (mtt90) REVERT: D 40 ARG cc_start: 0.6719 (tpt170) cc_final: 0.6430 (tpt170) REVERT: D 59 LYS cc_start: 0.7795 (mtpt) cc_final: 0.7507 (mtmt) REVERT: D 104 ARG cc_start: 0.7431 (ttm170) cc_final: 0.7211 (ttm-80) outliers start: 26 outliers final: 18 residues processed: 184 average time/residue: 0.1775 time to fit residues: 40.1631 Evaluate side-chains 184 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 166 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 20 HIS Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 45 PHE Chi-restraints excluded: chain D residue 84 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 46 optimal weight: 0.0050 chunk 37 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS C 58 HIS D 39 GLN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4699 Z= 0.198 Angle : 0.675 8.099 6449 Z= 0.322 Chirality : 0.043 0.218 700 Planarity : 0.006 0.079 806 Dihedral : 9.222 69.469 632 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 6.07 % Allowed : 26.46 % Favored : 67.46 % 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: 1.05 (0.36), residues: 566 helix: 1.18 (0.25), residues: 442 sheet: None (None), residues: 0 loop : -0.92 (0.61), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 37 HIS 0.007 0.001 HIS B 77 PHE 0.009 0.001 PHE B 85 TYR 0.008 0.001 TYR B 145 ARG 0.001 0.000 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 176 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6140 (tt0) cc_final: 0.5636 (tt0) REVERT: A 47 ASP cc_start: 0.6466 (t70) cc_final: 0.6162 (t0) REVERT: B 59 LYS cc_start: 0.7816 (mtpt) cc_final: 0.7564 (mtmt) REVERT: C 27 GLU cc_start: 0.6235 (tt0) cc_final: 0.5582 (tt0) REVERT: C 112 HIS cc_start: 0.6844 (m-70) cc_final: 0.6337 (m90) REVERT: D 30 ARG cc_start: 0.7892 (mtt-85) cc_final: 0.7679 (mtt180) REVERT: D 40 ARG cc_start: 0.6698 (tpt170) cc_final: 0.6482 (tpt170) REVERT: D 59 LYS cc_start: 0.7848 (mtpt) cc_final: 0.7571 (mtmt) REVERT: D 99 ASP cc_start: 0.7089 (t0) cc_final: 0.6448 (t70) outliers start: 28 outliers final: 20 residues processed: 189 average time/residue: 0.1739 time to fit residues: 40.4407 Evaluate side-chains 185 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 165 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 20 HIS Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 45 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS B 39 GLN C 58 HIS C 97 ASN D 39 GLN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4699 Z= 0.231 Angle : 0.719 9.468 6449 Z= 0.340 Chirality : 0.044 0.220 700 Planarity : 0.006 0.077 806 Dihedral : 9.247 69.860 631 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 6.29 % Allowed : 30.37 % Favored : 63.34 % 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: 1.11 (0.37), residues: 566 helix: 1.22 (0.25), residues: 440 sheet: None (None), residues: 0 loop : -0.84 (0.61), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 37 HIS 0.008 0.001 HIS D 77 PHE 0.010 0.001 PHE C 36 TYR 0.009 0.001 TYR B 35 ARG 0.002 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 163 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6136 (tt0) cc_final: 0.5764 (tt0) REVERT: A 47 ASP cc_start: 0.6437 (t70) cc_final: 0.6176 (t0) REVERT: B 59 LYS cc_start: 0.7848 (mtpt) cc_final: 0.7559 (mtmt) REVERT: C 27 GLU cc_start: 0.6251 (tt0) cc_final: 0.5672 (tt0) REVERT: D 30 ARG cc_start: 0.7999 (mtt-85) cc_final: 0.7764 (mtt180) REVERT: D 59 LYS cc_start: 0.7868 (mtpt) cc_final: 0.7631 (mtmt) outliers start: 29 outliers final: 26 residues processed: 178 average time/residue: 0.1860 time to fit residues: 40.5186 Evaluate side-chains 184 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 158 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 20 HIS Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 45 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS B 39 GLN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 HIS D 39 GLN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4699 Z= 0.207 Angle : 0.708 8.637 6449 Z= 0.333 Chirality : 0.043 0.201 700 Planarity : 0.006 0.076 806 Dihedral : 9.094 69.028 631 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.42 % Allowed : 30.59 % Favored : 63.99 % 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: 1.17 (0.37), residues: 566 helix: 1.31 (0.25), residues: 438 sheet: None (None), residues: 0 loop : -0.95 (0.60), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 37 HIS 0.009 0.001 HIS D 77 PHE 0.009 0.001 PHE B 85 TYR 0.008 0.001 TYR D 145 ARG 0.002 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6095 (tt0) cc_final: 0.5528 (tt0) REVERT: A 47 ASP cc_start: 0.6412 (t70) cc_final: 0.6138 (t0) REVERT: B 59 LYS cc_start: 0.7874 (mtpt) cc_final: 0.7634 (mtmt) REVERT: C 27 GLU cc_start: 0.6168 (tt0) cc_final: 0.5576 (tt0) REVERT: C 112 HIS cc_start: 0.6826 (m-70) cc_final: 0.6305 (m90) outliers start: 25 outliers final: 22 residues processed: 171 average time/residue: 0.1803 time to fit residues: 37.9176 Evaluate side-chains 175 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 153 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 20 HIS Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 45 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 47 optimal weight: 0.0670 chunk 50 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS B 39 GLN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 HIS C 97 ASN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4699 Z= 0.225 Angle : 0.724 8.865 6449 Z= 0.341 Chirality : 0.044 0.213 700 Planarity : 0.006 0.076 806 Dihedral : 9.142 70.179 631 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.77 % Allowed : 32.75 % Favored : 62.47 % 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: 1.17 (0.37), residues: 566 helix: 1.31 (0.25), residues: 438 sheet: None (None), residues: 0 loop : -0.98 (0.61), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 37 HIS 0.009 0.002 HIS D 77 PHE 0.009 0.001 PHE C 36 TYR 0.011 0.001 TYR D 35 ARG 0.004 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6119 (tt0) cc_final: 0.5477 (tt0) REVERT: A 47 ASP cc_start: 0.6378 (t70) cc_final: 0.6108 (t0) REVERT: A 112 HIS cc_start: 0.6877 (m-70) cc_final: 0.6397 (m-70) REVERT: A 118 THR cc_start: 0.7344 (p) cc_final: 0.6974 (m) REVERT: B 59 LYS cc_start: 0.7886 (mtpt) cc_final: 0.7628 (mtmt) REVERT: C 27 GLU cc_start: 0.6167 (tt0) cc_final: 0.5360 (tt0) REVERT: C 112 HIS cc_start: 0.6834 (m-70) cc_final: 0.5993 (m90) REVERT: D 99 ASP cc_start: 0.7570 (t70) cc_final: 0.7200 (t70) outliers start: 22 outliers final: 21 residues processed: 167 average time/residue: 0.1842 time to fit residues: 37.5659 Evaluate side-chains 173 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 45 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.9980 chunk 47 optimal weight: 0.0980 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS B 39 GLN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 HIS C 97 ASN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4699 Z= 0.242 Angle : 0.733 9.088 6449 Z= 0.348 Chirality : 0.045 0.217 700 Planarity : 0.006 0.076 806 Dihedral : 9.189 70.043 631 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 5.64 % Allowed : 33.41 % Favored : 60.95 % 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: 1.39 (0.37), residues: 566 helix: 1.51 (0.26), residues: 424 sheet: None (None), residues: 0 loop : -0.80 (0.58), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP D 37 HIS 0.009 0.001 HIS B 77 PHE 0.010 0.001 PHE A 36 TYR 0.012 0.001 TYR B 35 ARG 0.003 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 155 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6111 (tt0) cc_final: 0.5485 (tt0) REVERT: A 47 ASP cc_start: 0.6382 (t70) cc_final: 0.6102 (t0) REVERT: A 112 HIS cc_start: 0.6906 (m-70) cc_final: 0.6442 (m-70) REVERT: B 59 LYS cc_start: 0.7881 (mtpt) cc_final: 0.7672 (mtmt) REVERT: C 27 GLU cc_start: 0.6157 (tt0) cc_final: 0.5330 (tt0) REVERT: C 112 HIS cc_start: 0.6864 (m-70) cc_final: 0.6019 (m90) outliers start: 26 outliers final: 24 residues processed: 167 average time/residue: 0.1883 time to fit residues: 38.3619 Evaluate side-chains 175 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 45 PHE Chi-restraints excluded: chain D residue 84 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 35 optimal weight: 0.0050 chunk 47 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS B 39 GLN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 HIS C 97 ASN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4699 Z= 0.266 Angle : 0.757 12.021 6449 Z= 0.359 Chirality : 0.046 0.200 700 Planarity : 0.006 0.076 806 Dihedral : 9.316 70.386 631 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 5.64 % Allowed : 33.62 % Favored : 60.74 % 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: 1.03 (0.37), residues: 566 helix: 1.22 (0.25), residues: 440 sheet: None (None), residues: 0 loop : -1.09 (0.61), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 37 HIS 0.009 0.002 HIS D 77 PHE 0.011 0.001 PHE C 36 TYR 0.014 0.001 TYR B 35 ARG 0.003 0.000 ARG B 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.6389 (t70) cc_final: 0.6109 (t0) REVERT: A 112 HIS cc_start: 0.6911 (m-70) cc_final: 0.6609 (m-70) REVERT: B 59 LYS cc_start: 0.7881 (mtpt) cc_final: 0.7655 (mtmt) REVERT: C 27 GLU cc_start: 0.6143 (tt0) cc_final: 0.5450 (tt0) outliers start: 26 outliers final: 24 residues processed: 159 average time/residue: 0.1759 time to fit residues: 34.5561 Evaluate side-chains 170 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 45 PHE Chi-restraints excluded: chain D residue 84 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS B 39 GLN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 HIS C 97 ASN ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.133559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.112956 restraints weight = 12366.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.115025 restraints weight = 9469.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.116578 restraints weight = 7853.523| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4699 Z= 0.258 Angle : 0.775 12.435 6449 Z= 0.364 Chirality : 0.046 0.209 700 Planarity : 0.006 0.076 806 Dihedral : 9.325 69.993 631 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.99 % Allowed : 33.62 % Favored : 61.39 % 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: 0.99 (0.37), residues: 566 helix: 1.18 (0.25), residues: 440 sheet: None (None), residues: 0 loop : -1.06 (0.61), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 37 HIS 0.008 0.002 HIS C 122 PHE 0.013 0.001 PHE C 36 TYR 0.013 0.001 TYR B 35 ARG 0.002 0.000 ARG B 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1540.16 seconds wall clock time: 28 minutes 25.68 seconds (1705.68 seconds total)