Starting phenix.real_space_refine on Sun Mar 10 17:50:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqs_28544/03_2024/8eqs_28544_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqs_28544/03_2024/8eqs_28544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqs_28544/03_2024/8eqs_28544.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqs_28544/03_2024/8eqs_28544.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqs_28544/03_2024/8eqs_28544_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqs_28544/03_2024/8eqs_28544_neut_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 20 5.16 5 C 2406 2.51 5 N 570 2.21 5 O 656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A ASP 199": "OD1" <-> "OD2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "B ASP 199": "OD1" <-> "OD2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "C GLU 38": "OE1" <-> "OE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "D GLU 38": "OE1" <-> "OE2" Residue "D GLU 44": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3654 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1573 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 3, 'TRANS': 188} Chain breaks: 1 Chain: "B" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1573 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 3, 'TRANS': 188} Chain breaks: 1 Chain: "C" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 229 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "D" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 229 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Time building chain proxies: 2.47, per 1000 atoms: 0.68 Number of scatterers: 3654 At special positions: 0 Unit cell: (73.428, 64.988, 89.464, 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) S 20 16.00 P 2 15.00 O 656 8.00 N 570 7.00 C 2406 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=0, symmetry=0 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 745.9 milliseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 2 sheets defined 48.9% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 44 through 60 Processing helix chain 'A' and resid 68 through 99 removed outlier: 3.512A pdb=" N ALA A 72 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 133 Processing helix chain 'A' and resid 137 through 140 No H-bonds generated for 'chain 'A' and resid 137 through 140' Processing helix chain 'A' and resid 220 through 223 No H-bonds generated for 'chain 'A' and resid 220 through 223' Processing helix chain 'B' and resid 44 through 60 Processing helix chain 'B' and resid 68 through 99 removed outlier: 3.512A pdb=" N ALA B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 78 " --> pdb=" O TYR B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 133 Processing helix chain 'B' and resid 137 through 140 No H-bonds generated for 'chain 'B' and resid 137 through 140' Processing helix chain 'B' and resid 220 through 223 No H-bonds generated for 'chain 'B' and resid 220 through 223' Processing helix chain 'C' and resid 26 through 47 Proline residue: C 34 - end of helix removed outlier: 4.378A pdb=" N GLN C 37 " --> pdb=" O GLY C 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 47 Proline residue: D 34 - end of helix removed outlier: 4.378A pdb=" N GLN D 37 " --> pdb=" O GLY D 33 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 155 through 160 removed outlier: 5.812A pdb=" N HIS A 150 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N TYR A 200 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE A 232 " --> pdb=" O GLU A 215 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR A 217 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE A 230 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 155 through 160 removed outlier: 5.812A pdb=" N HIS B 150 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N TYR B 200 " --> pdb=" O HIS B 150 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE B 232 " --> pdb=" O GLU B 215 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR B 217 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE B 230 " --> pdb=" O THR B 217 " (cutoff:3.500A) 216 hydrogen bonds defined for protein. 624 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: 1.00 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 566 1.31 - 1.44: 1140 1.44 - 1.56: 2016 1.56 - 1.69: 4 1.69 - 1.81: 24 Bond restraints: 3750 Sorted by residual: bond pdb=" C10 PEE B 401 " pdb=" O2 PEE B 401 " ideal model delta sigma weight residual 1.332 1.424 -0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C10 PEE A 401 " pdb=" O2 PEE A 401 " ideal model delta sigma weight residual 1.332 1.423 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C30 PEE A 401 " pdb=" O3 PEE A 401 " ideal model delta sigma weight residual 1.327 1.411 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C30 PEE B 401 " pdb=" O3 PEE B 401 " ideal model delta sigma weight residual 1.327 1.410 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C10 PEE A 401 " pdb=" C11 PEE A 401 " ideal model delta sigma weight residual 1.504 1.549 -0.045 2.00e-02 2.50e+03 5.17e+00 ... (remaining 3745 not shown) Histogram of bond angle deviations from ideal: 100.78 - 107.44: 86 107.44 - 114.10: 2077 114.10 - 120.76: 1700 120.76 - 127.42: 1185 127.42 - 134.07: 38 Bond angle restraints: 5086 Sorted by residual: angle pdb=" O3P PEE B 401 " pdb=" P PEE B 401 " pdb=" O4P PEE B 401 " ideal model delta sigma weight residual 92.91 109.76 -16.85 3.00e+00 1.11e-01 3.15e+01 angle pdb=" O3P PEE A 401 " pdb=" P PEE A 401 " pdb=" O4P PEE A 401 " ideal model delta sigma weight residual 92.91 109.76 -16.85 3.00e+00 1.11e-01 3.15e+01 angle pdb=" O1P PEE A 401 " pdb=" P PEE A 401 " pdb=" O2P PEE A 401 " ideal model delta sigma weight residual 119.43 109.24 10.19 3.00e+00 1.11e-01 1.15e+01 angle pdb=" O1P PEE B 401 " pdb=" P PEE B 401 " pdb=" O2P PEE B 401 " ideal model delta sigma weight residual 119.43 109.24 10.19 3.00e+00 1.11e-01 1.15e+01 angle pdb=" C11 PEE B 401 " pdb=" C10 PEE B 401 " pdb=" O2 PEE B 401 " ideal model delta sigma weight residual 111.70 120.37 -8.67 3.00e+00 1.11e-01 8.35e+00 ... (remaining 5081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.50: 2070 31.50 - 63.00: 58 63.00 - 94.50: 12 94.50 - 126.00: 0 126.00 - 157.50: 6 Dihedral angle restraints: 2146 sinusoidal: 858 harmonic: 1288 Sorted by residual: dihedral pdb=" C3 PEE A 401 " pdb=" C1 PEE A 401 " pdb=" C2 PEE A 401 " pdb=" O3P PEE A 401 " ideal model delta sinusoidal sigma weight residual 62.73 -94.77 157.50 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C3 PEE B 401 " pdb=" C1 PEE B 401 " pdb=" C2 PEE B 401 " pdb=" O3P PEE B 401 " ideal model delta sinusoidal sigma weight residual 62.73 -94.74 157.47 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C2 PEE A 401 " pdb=" C10 PEE A 401 " pdb=" O2 PEE A 401 " pdb=" O4 PEE A 401 " ideal model delta sinusoidal sigma weight residual 2.73 -153.71 156.44 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 2143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 485 0.063 - 0.125: 61 0.125 - 0.188: 8 0.188 - 0.251: 0 0.251 - 0.314: 2 Chirality restraints: 556 Sorted by residual: chirality pdb=" C2 PEE B 401 " pdb=" C1 PEE B 401 " pdb=" C3 PEE B 401 " pdb=" O2 PEE B 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.64 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C2 PEE A 401 " pdb=" C1 PEE A 401 " pdb=" C3 PEE A 401 " pdb=" O2 PEE A 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.64 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA ILE A 186 " pdb=" N ILE A 186 " pdb=" C ILE A 186 " pdb=" CB ILE A 186 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 553 not shown) Planarity restraints: 622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 80 " 0.007 2.00e-02 2.50e+03 1.31e-02 1.73e+00 pdb=" C ILE A 80 " -0.023 2.00e-02 2.50e+03 pdb=" O ILE A 80 " 0.009 2.00e-02 2.50e+03 pdb=" N CYS A 81 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 80 " -0.007 2.00e-02 2.50e+03 1.31e-02 1.70e+00 pdb=" C ILE B 80 " 0.023 2.00e-02 2.50e+03 pdb=" O ILE B 80 " -0.009 2.00e-02 2.50e+03 pdb=" N CYS B 81 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 82 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.66e+00 pdb=" C ASN A 82 " 0.022 2.00e-02 2.50e+03 pdb=" O ASN A 82 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU A 83 " -0.007 2.00e-02 2.50e+03 ... (remaining 619 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 536 2.76 - 3.29: 3678 3.29 - 3.83: 6187 3.83 - 4.36: 7052 4.36 - 4.90: 12099 Nonbonded interactions: 29552 Sorted by model distance: nonbonded pdb=" OG SER A 58 " pdb=" NE2 GLN B 116 " model vdw 2.219 2.520 nonbonded pdb=" NE2 GLN A 116 " pdb=" OG SER B 58 " model vdw 2.219 2.520 nonbonded pdb=" OH TYR A 154 " pdb=" OE2 GLU A 191 " model vdw 2.247 2.440 nonbonded pdb=" OH TYR B 154 " pdb=" OE2 GLU B 191 " model vdw 2.247 2.440 nonbonded pdb=" OE1 GLU C 38 " pdb=" ND2 ASN C 42 " model vdw 2.258 2.520 ... (remaining 29547 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' selection = chain 'B' } ncs_group { reference = chain 'C' 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 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: 1.640 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: 3.450 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.630 Find NCS groups from input model: 0.330 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 : 0.005 0.092 3750 Z= 0.333 Angle : 0.737 16.848 5086 Z= 0.344 Chirality : 0.045 0.314 556 Planarity : 0.003 0.024 622 Dihedral : 19.168 157.496 1322 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 0.01 (0.38), residues: 426 helix: 1.25 (0.35), residues: 198 sheet: -0.34 (0.60), residues: 82 loop : -1.49 (0.38), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 131 HIS 0.002 0.001 HIS B 150 PHE 0.012 0.001 PHE A 56 TYR 0.004 0.001 TYR A 91 ARG 0.001 0.000 ARG D 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.416 Fit side-chains REVERT: A 45 TRP cc_start: 0.8227 (m100) cc_final: 0.7956 (m100) REVERT: A 67 LYS cc_start: 0.8728 (mmmm) cc_final: 0.8474 (mmmm) REVERT: A 87 PHE cc_start: 0.8744 (t80) cc_final: 0.8543 (t80) REVERT: A 130 CYS cc_start: 0.8322 (p) cc_final: 0.7785 (p) REVERT: A 136 LYS cc_start: 0.7947 (mmtt) cc_final: 0.7438 (mmtt) REVERT: A 152 HIS cc_start: 0.7813 (t-90) cc_final: 0.7579 (t70) REVERT: A 198 LYS cc_start: 0.8764 (mmtm) cc_final: 0.8446 (mmmm) REVERT: B 41 LEU cc_start: 0.8950 (mm) cc_final: 0.8687 (mt) REVERT: B 45 TRP cc_start: 0.8227 (m100) cc_final: 0.7955 (m100) REVERT: B 67 LYS cc_start: 0.8734 (mmmm) cc_final: 0.8478 (mmmm) REVERT: B 87 PHE cc_start: 0.8753 (t80) cc_final: 0.8545 (t80) REVERT: B 130 CYS cc_start: 0.8324 (p) cc_final: 0.7783 (p) REVERT: B 136 LYS cc_start: 0.7955 (mmtt) cc_final: 0.7446 (mmtt) REVERT: B 152 HIS cc_start: 0.7806 (t-90) cc_final: 0.7576 (t70) REVERT: B 198 LYS cc_start: 0.8765 (mmtm) cc_final: 0.8446 (mmmm) REVERT: C 25 PHE cc_start: 0.4370 (m-10) cc_final: 0.3971 (m-10) REVERT: C 42 ASN cc_start: 0.8145 (m-40) cc_final: 0.7757 (m-40) REVERT: D 25 PHE cc_start: 0.4364 (m-10) cc_final: 0.3958 (m-10) REVERT: D 42 ASN cc_start: 0.8143 (m-40) cc_final: 0.7756 (m-40) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1820 time to fit residues: 29.7154 Evaluate side-chains 121 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 0.2980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN A 185 GLN B 57 GLN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN B 185 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3750 Z= 0.233 Angle : 0.472 4.370 5086 Z= 0.263 Chirality : 0.042 0.152 556 Planarity : 0.003 0.023 622 Dihedral : 17.233 146.689 516 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.06 % Allowed : 9.02 % Favored : 88.92 % 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: 1.32 (0.39), residues: 426 helix: 2.58 (0.33), residues: 210 sheet: -0.73 (0.55), residues: 92 loop : -0.81 (0.46), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 149 HIS 0.003 0.001 HIS B 204 PHE 0.009 0.001 PHE B 56 TYR 0.013 0.001 TYR A 74 ARG 0.003 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 0.390 Fit side-chains REVERT: A 67 LYS cc_start: 0.8546 (mmmm) cc_final: 0.7947 (mmmm) REVERT: A 126 ARG cc_start: 0.8361 (mmm160) cc_final: 0.8110 (mmm160) REVERT: A 130 CYS cc_start: 0.8613 (p) cc_final: 0.7806 (p) REVERT: A 136 LYS cc_start: 0.7848 (mmtt) cc_final: 0.7467 (mmtt) REVERT: A 198 LYS cc_start: 0.8803 (mmtm) cc_final: 0.8468 (mmmm) REVERT: B 67 LYS cc_start: 0.8552 (mmmm) cc_final: 0.7952 (mmmm) REVERT: B 126 ARG cc_start: 0.8360 (mmm160) cc_final: 0.8107 (mmm160) REVERT: B 130 CYS cc_start: 0.8613 (p) cc_final: 0.7803 (p) REVERT: B 136 LYS cc_start: 0.7857 (mmtt) cc_final: 0.7476 (mmtt) REVERT: B 198 LYS cc_start: 0.8805 (mmtm) cc_final: 0.8469 (mmmm) REVERT: C 42 ASN cc_start: 0.8103 (m-40) cc_final: 0.7702 (m-40) REVERT: D 42 ASN cc_start: 0.8102 (m-40) cc_final: 0.7703 (m-40) outliers start: 8 outliers final: 6 residues processed: 125 average time/residue: 0.1929 time to fit residues: 28.3112 Evaluate side-chains 117 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 0.0000 chunk 38 optimal weight: 10.0000 chunk 41 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 0.2980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3750 Z= 0.155 Angle : 0.443 4.293 5086 Z= 0.245 Chirality : 0.040 0.139 556 Planarity : 0.003 0.023 622 Dihedral : 16.719 139.581 516 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.03 % Allowed : 13.40 % Favored : 85.57 % 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: 1.58 (0.40), residues: 426 helix: 3.17 (0.32), residues: 208 sheet: -0.63 (0.58), residues: 84 loop : -1.36 (0.42), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 149 HIS 0.002 0.001 HIS B 204 PHE 0.014 0.001 PHE B 207 TYR 0.009 0.001 TYR A 200 ARG 0.004 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 0.415 Fit side-chains REVERT: A 126 ARG cc_start: 0.8366 (mmm160) cc_final: 0.8116 (mmm160) REVERT: A 128 TRP cc_start: 0.8159 (t60) cc_final: 0.7519 (t60) REVERT: A 130 CYS cc_start: 0.8526 (p) cc_final: 0.7661 (p) REVERT: A 134 LYS cc_start: 0.8043 (mmtt) cc_final: 0.7807 (mmtt) REVERT: A 136 LYS cc_start: 0.7883 (mmtt) cc_final: 0.7498 (mmtt) REVERT: A 198 LYS cc_start: 0.8848 (mmtm) cc_final: 0.8489 (mmmm) REVERT: B 43 PHE cc_start: 0.7598 (m-10) cc_final: 0.7386 (m-80) REVERT: B 126 ARG cc_start: 0.8363 (mmm160) cc_final: 0.8115 (mmm160) REVERT: B 128 TRP cc_start: 0.8153 (t60) cc_final: 0.7513 (t60) REVERT: B 130 CYS cc_start: 0.8526 (p) cc_final: 0.7660 (p) REVERT: B 134 LYS cc_start: 0.8060 (mmtt) cc_final: 0.7841 (mmtt) REVERT: B 136 LYS cc_start: 0.7890 (mmtt) cc_final: 0.7505 (mmtt) REVERT: B 198 LYS cc_start: 0.8850 (mmtm) cc_final: 0.8490 (mmmm) REVERT: C 29 ARG cc_start: 0.7008 (ttt-90) cc_final: 0.6534 (mtt-85) REVERT: C 42 ASN cc_start: 0.8133 (m-40) cc_final: 0.7708 (m-40) REVERT: D 29 ARG cc_start: 0.7005 (ttt-90) cc_final: 0.6529 (mtt-85) REVERT: D 42 ASN cc_start: 0.8133 (m-40) cc_final: 0.7708 (m-40) outliers start: 4 outliers final: 4 residues processed: 122 average time/residue: 0.1991 time to fit residues: 28.5180 Evaluate side-chains 117 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 127 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3750 Z= 0.301 Angle : 0.478 4.409 5086 Z= 0.268 Chirality : 0.042 0.142 556 Planarity : 0.003 0.022 622 Dihedral : 16.763 144.194 516 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.61 % Allowed : 13.14 % Favored : 83.25 % 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: 1.71 (0.40), residues: 426 helix: 3.43 (0.33), residues: 208 sheet: -1.09 (0.55), residues: 88 loop : -1.16 (0.44), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 149 HIS 0.002 0.000 HIS B 204 PHE 0.009 0.002 PHE A 56 TYR 0.008 0.001 TYR A 109 ARG 0.003 0.000 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.397 Fit side-chains REVERT: A 126 ARG cc_start: 0.8379 (mmm160) cc_final: 0.8121 (mmm160) REVERT: A 130 CYS cc_start: 0.8668 (p) cc_final: 0.7804 (p) REVERT: A 198 LYS cc_start: 0.8827 (mmtm) cc_final: 0.8421 (mmmm) REVERT: B 43 PHE cc_start: 0.7747 (m-10) cc_final: 0.7444 (m-80) REVERT: B 126 ARG cc_start: 0.8378 (mmm160) cc_final: 0.8119 (mmm160) REVERT: B 130 CYS cc_start: 0.8668 (p) cc_final: 0.7805 (p) REVERT: B 198 LYS cc_start: 0.8829 (mmtm) cc_final: 0.8420 (mmmm) REVERT: C 42 ASN cc_start: 0.8204 (m-40) cc_final: 0.7781 (m-40) REVERT: D 42 ASN cc_start: 0.8203 (m-40) cc_final: 0.7782 (m-40) outliers start: 14 outliers final: 8 residues processed: 116 average time/residue: 0.1847 time to fit residues: 25.4746 Evaluate side-chains 108 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 78 GLN ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN B 57 GLN B 78 GLN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3750 Z= 0.183 Angle : 0.453 4.438 5086 Z= 0.250 Chirality : 0.040 0.135 556 Planarity : 0.003 0.023 622 Dihedral : 16.718 153.455 516 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.03 % Allowed : 15.98 % Favored : 82.99 % 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: 1.82 (0.40), residues: 426 helix: 3.55 (0.33), residues: 208 sheet: -1.07 (0.52), residues: 92 loop : -1.13 (0.44), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 149 HIS 0.002 0.000 HIS B 204 PHE 0.013 0.001 PHE B 207 TYR 0.008 0.001 TYR B 74 ARG 0.004 0.000 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 0.426 Fit side-chains REVERT: A 126 ARG cc_start: 0.8356 (mmm160) cc_final: 0.8043 (mmm160) REVERT: A 130 CYS cc_start: 0.8688 (p) cc_final: 0.7796 (p) REVERT: A 155 ASP cc_start: 0.8168 (m-30) cc_final: 0.7830 (t0) REVERT: A 198 LYS cc_start: 0.8863 (mmtm) cc_final: 0.8476 (mmmm) REVERT: B 43 PHE cc_start: 0.7777 (m-10) cc_final: 0.7473 (m-80) REVERT: B 126 ARG cc_start: 0.8356 (mmm160) cc_final: 0.8043 (mmm160) REVERT: B 130 CYS cc_start: 0.8679 (p) cc_final: 0.7793 (p) REVERT: B 155 ASP cc_start: 0.8168 (m-30) cc_final: 0.7832 (t0) REVERT: B 198 LYS cc_start: 0.8865 (mmtm) cc_final: 0.8476 (mmmm) REVERT: C 42 ASN cc_start: 0.8191 (m-40) cc_final: 0.7779 (m-40) REVERT: D 42 ASN cc_start: 0.8192 (m-40) cc_final: 0.7782 (m-40) outliers start: 4 outliers final: 2 residues processed: 111 average time/residue: 0.1867 time to fit residues: 24.6054 Evaluate side-chains 111 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.0980 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3750 Z= 0.194 Angle : 0.447 4.396 5086 Z= 0.250 Chirality : 0.040 0.139 556 Planarity : 0.003 0.023 622 Dihedral : 16.974 165.157 516 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.55 % Allowed : 14.95 % 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: 1.90 (0.40), residues: 426 helix: 3.58 (0.33), residues: 208 sheet: -1.00 (0.54), residues: 88 loop : -1.07 (0.43), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 149 HIS 0.001 0.000 HIS B 204 PHE 0.023 0.002 PHE A 105 TYR 0.008 0.001 TYR A 74 ARG 0.004 0.000 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 0.444 Fit side-chains REVERT: A 130 CYS cc_start: 0.8624 (p) cc_final: 0.8018 (p) REVERT: A 198 LYS cc_start: 0.8828 (mmtm) cc_final: 0.8442 (mmmm) REVERT: B 43 PHE cc_start: 0.7797 (m-10) cc_final: 0.7499 (m-80) REVERT: B 130 CYS cc_start: 0.8622 (p) cc_final: 0.8019 (p) REVERT: B 198 LYS cc_start: 0.8849 (mmtm) cc_final: 0.8469 (mmmm) REVERT: C 42 ASN cc_start: 0.8182 (m-40) cc_final: 0.7770 (m-40) REVERT: D 42 ASN cc_start: 0.8183 (m-40) cc_final: 0.7771 (m-40) outliers start: 6 outliers final: 6 residues processed: 111 average time/residue: 0.1828 time to fit residues: 24.2410 Evaluate side-chains 112 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3750 Z= 0.197 Angle : 0.456 5.111 5086 Z= 0.252 Chirality : 0.040 0.142 556 Planarity : 0.003 0.023 622 Dihedral : 17.414 174.399 516 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.06 % Allowed : 14.95 % Favored : 82.99 % 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: 1.94 (0.40), residues: 426 helix: 3.57 (0.32), residues: 208 sheet: -1.02 (0.53), residues: 92 loop : -0.91 (0.45), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 149 HIS 0.002 0.000 HIS B 204 PHE 0.028 0.002 PHE A 105 TYR 0.008 0.001 TYR B 74 ARG 0.004 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 0.420 Fit side-chains REVERT: A 130 CYS cc_start: 0.8651 (p) cc_final: 0.8057 (p) REVERT: A 198 LYS cc_start: 0.8826 (mmtm) cc_final: 0.8460 (mmmm) REVERT: B 43 PHE cc_start: 0.7772 (m-10) cc_final: 0.7506 (m-80) REVERT: B 130 CYS cc_start: 0.8649 (p) cc_final: 0.8053 (p) REVERT: B 198 LYS cc_start: 0.8826 (mmtm) cc_final: 0.8457 (mmmm) REVERT: C 42 ASN cc_start: 0.8077 (m-40) cc_final: 0.7659 (m-40) REVERT: D 42 ASN cc_start: 0.8074 (m-40) cc_final: 0.7657 (m-40) outliers start: 8 outliers final: 6 residues processed: 113 average time/residue: 0.1672 time to fit residues: 22.8456 Evaluate side-chains 114 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 0.0370 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 82 ASN B 78 GLN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3750 Z= 0.180 Angle : 0.451 5.400 5086 Z= 0.248 Chirality : 0.040 0.147 556 Planarity : 0.003 0.023 622 Dihedral : 17.611 178.056 516 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.80 % Allowed : 14.95 % Favored : 83.25 % 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: 2.09 (0.40), residues: 426 helix: 3.61 (0.32), residues: 208 sheet: -0.62 (0.55), residues: 88 loop : -0.97 (0.45), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 149 HIS 0.002 0.000 HIS A 204 PHE 0.025 0.002 PHE B 207 TYR 0.008 0.001 TYR A 74 ARG 0.003 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 0.427 Fit side-chains REVERT: A 104 GLN cc_start: 0.9276 (mt0) cc_final: 0.8889 (tt0) REVERT: A 130 CYS cc_start: 0.8643 (p) cc_final: 0.8054 (p) REVERT: A 198 LYS cc_start: 0.8805 (mmtm) cc_final: 0.8429 (mmmm) REVERT: A 199 ASP cc_start: 0.8592 (p0) cc_final: 0.8348 (p0) REVERT: B 43 PHE cc_start: 0.7761 (m-10) cc_final: 0.7498 (m-80) REVERT: B 130 CYS cc_start: 0.8650 (p) cc_final: 0.8057 (p) REVERT: B 198 LYS cc_start: 0.8806 (mmtm) cc_final: 0.8428 (mmmm) REVERT: B 199 ASP cc_start: 0.8597 (p0) cc_final: 0.8349 (p0) REVERT: B 209 GLU cc_start: 0.8365 (tt0) cc_final: 0.7866 (tp30) REVERT: C 42 ASN cc_start: 0.8140 (m-40) cc_final: 0.7724 (m-40) REVERT: D 42 ASN cc_start: 0.8139 (m-40) cc_final: 0.7725 (m-40) outliers start: 7 outliers final: 6 residues processed: 115 average time/residue: 0.1680 time to fit residues: 23.4237 Evaluate side-chains 117 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 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 78 GLN ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3750 Z= 0.215 Angle : 0.461 4.388 5086 Z= 0.255 Chirality : 0.041 0.149 556 Planarity : 0.003 0.023 622 Dihedral : 17.700 179.272 516 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.55 % Allowed : 15.72 % Favored : 82.73 % 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: 2.04 (0.40), residues: 426 helix: 3.54 (0.32), residues: 208 sheet: -0.91 (0.54), residues: 92 loop : -0.70 (0.47), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 149 HIS 0.002 0.000 HIS A 204 PHE 0.023 0.002 PHE A 105 TYR 0.011 0.001 TYR A 145 ARG 0.004 0.001 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 0.420 Fit side-chains REVERT: A 130 CYS cc_start: 0.8530 (p) cc_final: 0.7909 (p) REVERT: A 198 LYS cc_start: 0.8789 (mmtm) cc_final: 0.8441 (mmmm) REVERT: A 209 GLU cc_start: 0.8567 (tt0) cc_final: 0.8123 (tp30) REVERT: B 43 PHE cc_start: 0.7734 (m-10) cc_final: 0.7461 (m-80) REVERT: B 130 CYS cc_start: 0.8534 (p) cc_final: 0.7914 (p) REVERT: B 198 LYS cc_start: 0.8790 (mmtm) cc_final: 0.8443 (mmmm) REVERT: C 42 ASN cc_start: 0.8178 (m-40) cc_final: 0.7743 (m-40) REVERT: D 42 ASN cc_start: 0.8175 (m-40) cc_final: 0.7741 (m-40) outliers start: 6 outliers final: 6 residues processed: 118 average time/residue: 0.1733 time to fit residues: 24.4789 Evaluate side-chains 119 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 113 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 0.2980 chunk 6 optimal weight: 0.0040 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3750 Z= 0.163 Angle : 0.460 6.183 5086 Z= 0.250 Chirality : 0.040 0.146 556 Planarity : 0.003 0.023 622 Dihedral : 17.337 175.006 516 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.55 % Allowed : 15.98 % Favored : 82.47 % 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: 2.12 (0.40), residues: 426 helix: 3.49 (0.32), residues: 208 sheet: -0.38 (0.58), residues: 84 loop : -0.86 (0.44), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 149 HIS 0.002 0.000 HIS A 204 PHE 0.028 0.002 PHE B 207 TYR 0.010 0.001 TYR A 74 ARG 0.004 0.000 ARG B 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 0.389 Fit side-chains REVERT: A 78 GLN cc_start: 0.8667 (mt0) cc_final: 0.8460 (mt0) REVERT: A 130 CYS cc_start: 0.8499 (p) cc_final: 0.7844 (p) REVERT: A 198 LYS cc_start: 0.8798 (mmtm) cc_final: 0.8449 (mmmm) REVERT: A 209 GLU cc_start: 0.8577 (tt0) cc_final: 0.8268 (tp30) REVERT: B 43 PHE cc_start: 0.7731 (m-10) cc_final: 0.7473 (m-80) REVERT: B 78 GLN cc_start: 0.8676 (mt0) cc_final: 0.8470 (mt0) REVERT: B 130 CYS cc_start: 0.8557 (p) cc_final: 0.7944 (p) REVERT: B 198 LYS cc_start: 0.8797 (mmtm) cc_final: 0.8447 (mmmm) REVERT: B 209 GLU cc_start: 0.8300 (tt0) cc_final: 0.8087 (tt0) REVERT: C 42 ASN cc_start: 0.8143 (m-40) cc_final: 0.7732 (m-40) REVERT: D 42 ASN cc_start: 0.8142 (m-40) cc_final: 0.7732 (m-40) outliers start: 6 outliers final: 6 residues processed: 118 average time/residue: 0.1693 time to fit residues: 24.0017 Evaluate side-chains 117 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.3980 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 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 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.114848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.086094 restraints weight = 5909.070| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.10 r_work: 0.2943 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3750 Z= 0.213 Angle : 0.471 6.017 5086 Z= 0.260 Chirality : 0.041 0.152 556 Planarity : 0.003 0.024 622 Dihedral : 16.905 169.495 516 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.80 % Allowed : 15.21 % Favored : 82.99 % 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: 2.08 (0.41), residues: 426 helix: 3.25 (0.33), residues: 220 sheet: -0.72 (0.55), residues: 92 loop : -0.60 (0.50), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 149 HIS 0.002 0.000 HIS A 204 PHE 0.021 0.001 PHE B 105 TYR 0.010 0.001 TYR B 74 ARG 0.005 0.001 ARG B 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1311.87 seconds wall clock time: 24 minutes 20.61 seconds (1460.61 seconds total)