Starting phenix.real_space_refine on Wed Jan 17 16:26:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0j_14223/01_2024/7r0j_14223_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0j_14223/01_2024/7r0j_14223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0j_14223/01_2024/7r0j_14223.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0j_14223/01_2024/7r0j_14223.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0j_14223/01_2024/7r0j_14223_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0j_14223/01_2024/7r0j_14223_updated.pdb" } resolution = 4.23 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= 0.019 sd= 0.045 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 6 5.49 5 S 19 5.16 5 C 2947 2.51 5 N 793 2.21 5 O 904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 118": "OE1" <-> "OE2" Residue "D TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 4669 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2815 Classifications: {'peptide': 354} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 325} Chain breaks: 1 Chain: "D" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1750 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 220} Chain breaks: 1 Time building chain proxies: 3.01, per 1000 atoms: 0.64 Number of scatterers: 4669 At special positions: 0 Unit cell: (87.04, 99.84, 88.32, 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 19 16.00 P 6 15.00 O 904 8.00 N 793 7.00 C 2947 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 91 " distance=2.03 Simple disulfide: pdb=" SG CYS D 103 " - pdb=" SG CYS D 170 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 222 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 881.1 milliseconds 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1122 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 5 helices and 12 sheets defined 3.7% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'C' and resid 99 through 108 Processing helix chain 'C' and resid 279 through 281 No H-bonds generated for 'chain 'C' and resid 279 through 281' Processing helix chain 'D' and resid 155 through 157 No H-bonds generated for 'chain 'D' and resid 155 through 157' Processing helix chain 'D' and resid 188 through 190 No H-bonds generated for 'chain 'D' and resid 188 through 190' Processing helix chain 'D' and resid 214 through 216 No H-bonds generated for 'chain 'D' and resid 214 through 216' Processing sheet with id= A, first strand: chain 'C' and resid 9 through 12 Processing sheet with id= B, first strand: chain 'C' and resid 26 through 28 removed outlier: 7.526A pdb=" N ARG C 169 " --> pdb=" O PHE C 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'C' and resid 76 through 78 Processing sheet with id= D, first strand: chain 'C' and resid 127 through 129 Processing sheet with id= E, first strand: chain 'C' and resid 183 through 188 Processing sheet with id= F, first strand: chain 'C' and resid 343 through 349 removed outlier: 3.811A pdb=" N TYR C 321 " --> pdb=" O PHE C 349 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLN C 237 " --> pdb=" O PRO C 252 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA C 239 " --> pdb=" O LYS C 250 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS C 250 " --> pdb=" O ALA C 239 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 53 through 59 removed outlier: 6.254A pdb=" N VAL C 55 " --> pdb=" O GLN C 85 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N GLN C 85 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU C 57 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASN C 83 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N CYS C 59 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N VAL C 81 " --> pdb=" O CYS C 59 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 7 through 9 Processing sheet with id= I, first strand: chain 'D' and resid 13 through 15 removed outlier: 5.567A pdb=" N LYS D 106 " --> pdb=" O LEU D 14 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 88 through 93 removed outlier: 5.764A pdb=" N GLN D 40 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU D 49 " --> pdb=" O GLN D 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 129 through 133 Processing sheet with id= L, first strand: chain 'D' and resid 136 through 138 removed outlier: 5.925A pdb=" N ARG D 164 " --> pdb=" O TRP D 173 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TRP D 173 " --> pdb=" O ARG D 164 " (cutoff:3.500A) 146 hydrogen bonds defined for protein. 384 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: 1.23 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1499 1.34 - 1.46: 1124 1.46 - 1.58: 2103 1.58 - 1.70: 22 1.70 - 1.82: 24 Bond restraints: 4772 Sorted by residual: bond pdb=" OG1 TPO A 360 " pdb=" P TPO A 360 " ideal model delta sigma weight residual 1.717 1.602 0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" OG1 TPO A 359 " pdb=" P TPO A 359 " ideal model delta sigma weight residual 1.717 1.616 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C ASN C 122 " pdb=" N LEU C 123 " ideal model delta sigma weight residual 1.331 1.257 0.075 1.59e-02 3.96e+03 2.21e+01 bond pdb=" O1P TPO A 359 " pdb=" P TPO A 359 " ideal model delta sigma weight residual 1.525 1.609 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" O1P TPO A 360 " pdb=" P TPO A 360 " ideal model delta sigma weight residual 1.525 1.608 -0.083 2.00e-02 2.50e+03 1.72e+01 ... (remaining 4767 not shown) Histogram of bond angle deviations from ideal: 94.97 - 102.81: 19 102.81 - 110.64: 1630 110.64 - 118.48: 2132 118.48 - 126.32: 2643 126.32 - 134.15: 62 Bond angle restraints: 6486 Sorted by residual: angle pdb=" C GLN D 41 " pdb=" N LYS D 42 " pdb=" CA LYS D 42 " ideal model delta sigma weight residual 121.80 134.13 -12.33 2.44e+00 1.68e-01 2.55e+01 angle pdb=" CB TPO A 360 " pdb=" OG1 TPO A 360 " pdb=" P TPO A 360 " ideal model delta sigma weight residual 119.31 105.14 14.17 3.00e+00 1.11e-01 2.23e+01 angle pdb=" N GLY C 141 " pdb=" CA GLY C 141 " pdb=" C GLY C 141 " ideal model delta sigma weight residual 110.74 117.04 -6.30 1.37e+00 5.33e-01 2.11e+01 angle pdb=" N LYS C 49 " pdb=" CA LYS C 49 " pdb=" C LYS C 49 " ideal model delta sigma weight residual 114.31 108.80 5.51 1.29e+00 6.01e-01 1.82e+01 angle pdb=" N ASP C 259 " pdb=" CA ASP C 259 " pdb=" C ASP C 259 " ideal model delta sigma weight residual 112.97 109.15 3.82 1.06e+00 8.90e-01 1.30e+01 ... (remaining 6481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 2650 17.88 - 35.77: 205 35.77 - 53.65: 30 53.65 - 71.53: 5 71.53 - 89.41: 6 Dihedral angle restraints: 2896 sinusoidal: 1152 harmonic: 1744 Sorted by residual: dihedral pdb=" CB CYS D 26 " pdb=" SG CYS D 26 " pdb=" SG CYS D 91 " pdb=" CB CYS D 91 " ideal model delta sinusoidal sigma weight residual 93.00 49.57 43.43 1 1.00e+01 1.00e-02 2.63e+01 dihedral pdb=" CA ARG D 226 " pdb=" C ARG D 226 " pdb=" N GLN D 227 " pdb=" CA GLN D 227 " ideal model delta harmonic sigma weight residual 180.00 -158.12 -21.88 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA LYS C 17 " pdb=" C LYS C 17 " pdb=" N LEU C 18 " pdb=" CA LEU C 18 " ideal model delta harmonic sigma weight residual -180.00 -158.30 -21.70 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 2893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 433 0.035 - 0.069: 180 0.069 - 0.103: 86 0.103 - 0.138: 23 0.138 - 0.172: 5 Chirality restraints: 727 Sorted by residual: chirality pdb=" CG LEU D 76 " pdb=" CB LEU D 76 " pdb=" CD1 LEU D 76 " pdb=" CD2 LEU D 76 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CA VAL C 81 " pdb=" N VAL C 81 " pdb=" C VAL C 81 " pdb=" CB VAL C 81 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA VAL C 220 " pdb=" N VAL C 220 " pdb=" C VAL C 220 " pdb=" CB VAL C 220 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.45e-01 ... (remaining 724 not shown) Planarity restraints: 825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 236 " -0.011 2.00e-02 2.50e+03 1.62e-02 6.56e+00 pdb=" CG TRP D 236 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP D 236 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP D 236 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 236 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 236 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 236 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 236 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 236 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP D 236 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 229 " 0.010 2.00e-02 2.50e+03 1.39e-02 4.86e+00 pdb=" CG TRP D 229 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP D 229 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 229 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 229 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP D 229 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 229 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 229 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 229 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 229 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 195 " -0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO C 196 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 196 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 196 " -0.026 5.00e-02 4.00e+02 ... (remaining 822 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 126 2.60 - 3.18: 4602 3.18 - 3.75: 7652 3.75 - 4.33: 10290 4.33 - 4.90: 15830 Nonbonded interactions: 38500 Sorted by model distance: nonbonded pdb=" O ASP D 85 " pdb=" OH TYR D 89 " model vdw 2.029 2.440 nonbonded pdb=" NE2 GLN D 92 " pdb=" O GLN D 93 " model vdw 2.186 2.520 nonbonded pdb=" N GLN C 130 " pdb=" O LEU C 287 " model vdw 2.188 2.520 nonbonded pdb=" O ALA C 263 " pdb=" OG SER C 266 " model vdw 2.191 2.440 nonbonded pdb=" O SER D 178 " pdb=" N GLY D 182 " model vdw 2.193 2.520 ... (remaining 38495 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.810 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.890 Find NCS groups from input model: 0.120 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 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 0.115 4772 Z= 0.495 Angle : 1.034 14.169 6486 Z= 0.554 Chirality : 0.048 0.172 727 Planarity : 0.006 0.055 825 Dihedral : 13.438 89.415 1765 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 37.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.20 % Allowed : 0.00 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.35), residues: 577 helix: -1.30 (1.09), residues: 17 sheet: -0.35 (0.34), residues: 245 loop : -0.80 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.006 TRP D 236 HIS 0.007 0.002 HIS C 111 PHE 0.023 0.003 PHE D 228 TYR 0.027 0.003 TYR D 90 ARG 0.011 0.001 ARG C 312 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 28 VAL cc_start: 0.8876 (t) cc_final: 0.8454 (t) REVERT: C 34 VAL cc_start: 0.8547 (t) cc_final: 0.8173 (t) REVERT: C 63 TYR cc_start: 0.7302 (t80) cc_final: 0.7023 (t80) REVERT: C 69 ASP cc_start: 0.8904 (m-30) cc_final: 0.8660 (m-30) REVERT: C 166 LEU cc_start: 0.9118 (tt) cc_final: 0.8798 (mt) REVERT: C 255 MET cc_start: 0.7974 (tpt) cc_final: 0.7742 (tpt) REVERT: C 272 TYR cc_start: 0.8115 (m-80) cc_final: 0.7478 (m-80) REVERT: D 64 ARG cc_start: 0.8462 (mmt180) cc_final: 0.8195 (mmm160) REVERT: D 101 PHE cc_start: 0.9469 (m-80) cc_final: 0.8723 (m-80) REVERT: D 209 MET cc_start: 0.9112 (mpp) cc_final: 0.8326 (mpp) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.1701 time to fit residues: 23.6011 Evaluate side-chains 84 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4772 Z= 0.205 Angle : 0.637 7.080 6486 Z= 0.320 Chirality : 0.043 0.139 727 Planarity : 0.004 0.040 825 Dihedral : 7.983 84.371 667 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 23.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.75 (0.35), residues: 577 helix: -0.67 (1.27), residues: 17 sheet: -0.05 (0.34), residues: 237 loop : -0.79 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP D 229 HIS 0.005 0.001 HIS C 198 PHE 0.013 0.002 PHE D 101 TYR 0.014 0.002 TYR D 90 ARG 0.005 0.001 ARG C 312 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 37 VAL cc_start: 0.9436 (t) cc_final: 0.9187 (t) REVERT: C 63 TYR cc_start: 0.6964 (t80) cc_final: 0.6742 (t80) REVERT: C 117 PHE cc_start: 0.7866 (m-80) cc_final: 0.7358 (m-80) REVERT: C 272 TYR cc_start: 0.7835 (m-80) cc_final: 0.7051 (m-80) REVERT: C 327 LEU cc_start: 0.9716 (mt) cc_final: 0.9452 (mt) REVERT: C 350 THR cc_start: 0.9320 (p) cc_final: 0.9099 (t) REVERT: C 352 MET cc_start: 0.8690 (ppp) cc_final: 0.8444 (ppp) REVERT: D 64 ARG cc_start: 0.8414 (mmt180) cc_final: 0.8168 (mmm160) REVERT: D 101 PHE cc_start: 0.9517 (m-80) cc_final: 0.9179 (m-80) REVERT: D 209 MET cc_start: 0.9220 (mpp) cc_final: 0.8850 (mpp) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1522 time to fit residues: 21.1081 Evaluate side-chains 83 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 HIS ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 4772 Z= 0.431 Angle : 0.813 10.234 6486 Z= 0.412 Chirality : 0.044 0.151 727 Planarity : 0.005 0.045 825 Dihedral : 8.365 80.676 667 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 37.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.28 (0.34), residues: 577 helix: -1.75 (1.03), residues: 17 sheet: -0.76 (0.31), residues: 246 loop : -0.77 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP D 236 HIS 0.007 0.002 HIS C 198 PHE 0.032 0.003 PHE D 228 TYR 0.020 0.003 TYR D 90 ARG 0.005 0.001 ARG C 285 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 VAL cc_start: 0.8661 (t) cc_final: 0.8400 (t) REVERT: C 69 ASP cc_start: 0.8153 (m-30) cc_final: 0.7871 (m-30) REVERT: C 166 LEU cc_start: 0.9014 (tt) cc_final: 0.8641 (mt) REVERT: C 272 TYR cc_start: 0.7910 (m-80) cc_final: 0.6997 (m-80) REVERT: C 327 LEU cc_start: 0.9671 (mt) cc_final: 0.9389 (mt) REVERT: C 352 MET cc_start: 0.8369 (ppp) cc_final: 0.8020 (ppp) REVERT: D 101 PHE cc_start: 0.9505 (m-80) cc_final: 0.9074 (m-80) REVERT: D 146 LEU cc_start: 0.8690 (mt) cc_final: 0.8422 (mt) REVERT: D 209 MET cc_start: 0.9032 (mpp) cc_final: 0.8699 (mpp) REVERT: D 216 ASP cc_start: 0.8614 (m-30) cc_final: 0.8379 (m-30) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1526 time to fit residues: 19.1834 Evaluate side-chains 72 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4772 Z= 0.258 Angle : 0.661 8.482 6486 Z= 0.334 Chirality : 0.042 0.135 727 Planarity : 0.005 0.049 825 Dihedral : 8.039 81.903 667 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 27.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.16 (0.35), residues: 577 helix: -1.01 (1.18), residues: 17 sheet: -0.73 (0.31), residues: 243 loop : -0.69 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP D 38 HIS 0.003 0.001 HIS D 161 PHE 0.019 0.002 PHE D 228 TYR 0.012 0.002 TYR D 230 ARG 0.005 0.001 ARG C 363 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 TYR cc_start: 0.8345 (m-10) cc_final: 0.8080 (m-10) REVERT: C 34 VAL cc_start: 0.8564 (t) cc_final: 0.8258 (t) REVERT: C 69 ASP cc_start: 0.8132 (m-30) cc_final: 0.7878 (m-30) REVERT: C 233 ILE cc_start: 0.9339 (mp) cc_final: 0.9097 (mp) REVERT: C 255 MET cc_start: 0.8340 (tpt) cc_final: 0.8140 (tpp) REVERT: C 272 TYR cc_start: 0.7879 (m-80) cc_final: 0.7154 (m-80) REVERT: C 350 THR cc_start: 0.9342 (p) cc_final: 0.9111 (t) REVERT: C 352 MET cc_start: 0.8014 (ppp) cc_final: 0.7627 (ppp) REVERT: D 101 PHE cc_start: 0.9558 (m-80) cc_final: 0.9184 (m-80) REVERT: D 146 LEU cc_start: 0.8695 (mt) cc_final: 0.8413 (mt) REVERT: D 209 MET cc_start: 0.9148 (mpp) cc_final: 0.8692 (mpp) REVERT: D 236 TRP cc_start: 0.8493 (m-10) cc_final: 0.8112 (m-10) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1508 time to fit residues: 19.8736 Evaluate side-chains 81 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 14 optimal weight: 0.3980 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 HIS ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4772 Z= 0.238 Angle : 0.640 8.264 6486 Z= 0.321 Chirality : 0.042 0.137 727 Planarity : 0.004 0.051 825 Dihedral : 7.943 82.175 667 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 25.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.09 (0.35), residues: 577 helix: -0.97 (1.13), residues: 17 sheet: -0.64 (0.32), residues: 238 loop : -0.68 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 236 HIS 0.003 0.001 HIS C 198 PHE 0.021 0.002 PHE D 74 TYR 0.010 0.002 TYR D 156 ARG 0.005 0.001 ARG C 363 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 VAL cc_start: 0.9385 (t) cc_final: 0.9183 (p) REVERT: C 69 ASP cc_start: 0.8140 (m-30) cc_final: 0.7884 (m-30) REVERT: C 233 ILE cc_start: 0.9301 (mp) cc_final: 0.8927 (mp) REVERT: C 255 MET cc_start: 0.8330 (tpt) cc_final: 0.8110 (tpp) REVERT: C 272 TYR cc_start: 0.7889 (m-80) cc_final: 0.7089 (m-80) REVERT: C 327 LEU cc_start: 0.9679 (mt) cc_final: 0.9369 (mt) REVERT: C 350 THR cc_start: 0.9348 (p) cc_final: 0.9117 (t) REVERT: D 84 GLU cc_start: 0.8487 (pm20) cc_final: 0.8235 (pm20) REVERT: D 101 PHE cc_start: 0.9517 (m-80) cc_final: 0.9093 (m-80) REVERT: D 146 LEU cc_start: 0.8646 (mt) cc_final: 0.8434 (mt) REVERT: D 209 MET cc_start: 0.9117 (mpp) cc_final: 0.8657 (mpp) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1479 time to fit residues: 20.3426 Evaluate side-chains 80 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 25 optimal weight: 30.0000 chunk 4 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 31 optimal weight: 0.0170 chunk 40 optimal weight: 2.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN C 353 HIS ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4772 Z= 0.239 Angle : 0.657 7.994 6486 Z= 0.329 Chirality : 0.042 0.143 727 Planarity : 0.004 0.049 825 Dihedral : 7.936 81.924 667 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 25.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.01 (0.35), residues: 577 helix: -0.78 (1.21), residues: 17 sheet: -0.65 (0.31), residues: 243 loop : -0.58 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 236 HIS 0.003 0.001 HIS D 161 PHE 0.016 0.002 PHE D 74 TYR 0.010 0.002 TYR C 113 ARG 0.005 0.001 ARG C 363 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 VAL cc_start: 0.9344 (t) cc_final: 0.9131 (p) REVERT: C 69 ASP cc_start: 0.8156 (m-30) cc_final: 0.7903 (m-30) REVERT: C 117 PHE cc_start: 0.8078 (m-80) cc_final: 0.7573 (m-80) REVERT: C 233 ILE cc_start: 0.9297 (mp) cc_final: 0.8883 (mp) REVERT: C 255 MET cc_start: 0.8183 (tpt) cc_final: 0.7829 (tpp) REVERT: C 272 TYR cc_start: 0.7844 (m-80) cc_final: 0.7128 (m-80) REVERT: C 327 LEU cc_start: 0.9666 (mt) cc_final: 0.9412 (mt) REVERT: C 350 THR cc_start: 0.9349 (p) cc_final: 0.9120 (t) REVERT: D 101 PHE cc_start: 0.9463 (m-80) cc_final: 0.9171 (m-80) REVERT: D 146 LEU cc_start: 0.8602 (mt) cc_final: 0.8350 (mt) REVERT: D 156 TYR cc_start: 0.8371 (m-10) cc_final: 0.8009 (m-10) REVERT: D 209 MET cc_start: 0.9081 (mpp) cc_final: 0.8662 (mpp) REVERT: D 229 TRP cc_start: 0.8376 (m100) cc_final: 0.8101 (m100) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1368 time to fit residues: 17.8300 Evaluate side-chains 80 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 HIS ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 HIS ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 4772 Z= 0.380 Angle : 0.761 8.719 6486 Z= 0.388 Chirality : 0.045 0.204 727 Planarity : 0.005 0.045 825 Dihedral : 8.376 81.190 667 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 35.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.27 (0.34), residues: 577 helix: -1.50 (1.15), residues: 17 sheet: -0.77 (0.31), residues: 245 loop : -0.78 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP D 229 HIS 0.012 0.002 HIS C 353 PHE 0.029 0.003 PHE D 74 TYR 0.020 0.003 TYR C 21 ARG 0.006 0.001 ARG C 363 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 233 ILE cc_start: 0.9251 (mp) cc_final: 0.8904 (mp) REVERT: C 272 TYR cc_start: 0.7881 (m-80) cc_final: 0.7232 (m-80) REVERT: C 327 LEU cc_start: 0.9671 (mt) cc_final: 0.9369 (mt) REVERT: D 101 PHE cc_start: 0.9465 (m-80) cc_final: 0.9148 (m-80) REVERT: D 146 LEU cc_start: 0.8595 (mt) cc_final: 0.8348 (mt) REVERT: D 209 MET cc_start: 0.9119 (mpp) cc_final: 0.8773 (mpp) REVERT: D 229 TRP cc_start: 0.8363 (m100) cc_final: 0.7687 (m100) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1514 time to fit residues: 18.0410 Evaluate side-chains 67 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 181 GLN C 198 HIS ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4772 Z= 0.199 Angle : 0.659 8.389 6486 Z= 0.329 Chirality : 0.044 0.150 727 Planarity : 0.004 0.046 825 Dihedral : 7.981 82.802 667 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 24.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.12 (0.34), residues: 577 helix: -1.27 (1.10), residues: 17 sheet: -0.62 (0.32), residues: 239 loop : -0.72 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP D 38 HIS 0.008 0.001 HIS C 210 PHE 0.019 0.002 PHE D 74 TYR 0.013 0.002 TYR C 113 ARG 0.006 0.001 ARG C 363 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 VAL cc_start: 0.9334 (t) cc_final: 0.9091 (p) REVERT: C 69 ASP cc_start: 0.8144 (m-30) cc_final: 0.7889 (m-30) REVERT: C 117 PHE cc_start: 0.8067 (m-80) cc_final: 0.7576 (m-80) REVERT: C 233 ILE cc_start: 0.9326 (mp) cc_final: 0.9024 (mp) REVERT: C 272 TYR cc_start: 0.7768 (m-80) cc_final: 0.7163 (m-80) REVERT: C 327 LEU cc_start: 0.9664 (mt) cc_final: 0.9412 (mt) REVERT: D 101 PHE cc_start: 0.9475 (m-80) cc_final: 0.9170 (m-80) REVERT: D 156 TYR cc_start: 0.8378 (m-10) cc_final: 0.7975 (m-10) REVERT: D 209 MET cc_start: 0.8596 (mpp) cc_final: 0.8278 (mpp) REVERT: D 229 TRP cc_start: 0.8179 (m100) cc_final: 0.7804 (m100) REVERT: D 236 TRP cc_start: 0.8493 (m-10) cc_final: 0.8004 (m-10) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1678 time to fit residues: 21.1665 Evaluate side-chains 81 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 HIS ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4772 Z= 0.238 Angle : 0.677 8.148 6486 Z= 0.341 Chirality : 0.044 0.141 727 Planarity : 0.004 0.046 825 Dihedral : 7.998 82.393 667 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 26.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.34), residues: 577 helix: -1.63 (0.99), residues: 23 sheet: -0.50 (0.32), residues: 232 loop : -0.67 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.006 TRP D 38 HIS 0.004 0.001 HIS C 210 PHE 0.015 0.002 PHE D 74 TYR 0.018 0.002 TYR C 63 ARG 0.005 0.000 ARG C 363 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 VAL cc_start: 0.9347 (t) cc_final: 0.9097 (p) REVERT: C 117 PHE cc_start: 0.8080 (m-80) cc_final: 0.7539 (m-80) REVERT: C 232 LYS cc_start: 0.9149 (mmpt) cc_final: 0.8932 (mmmt) REVERT: C 233 ILE cc_start: 0.9318 (mp) cc_final: 0.9004 (mp) REVERT: C 272 TYR cc_start: 0.7696 (m-80) cc_final: 0.7136 (m-80) REVERT: C 327 LEU cc_start: 0.9675 (mt) cc_final: 0.9462 (mt) REVERT: C 352 MET cc_start: 0.8486 (ppp) cc_final: 0.8225 (ppp) REVERT: D 86 PHE cc_start: 0.8383 (m-80) cc_final: 0.7602 (m-80) REVERT: D 101 PHE cc_start: 0.9523 (m-80) cc_final: 0.9246 (m-80) REVERT: D 209 MET cc_start: 0.8723 (mpp) cc_final: 0.8414 (mpp) REVERT: D 229 TRP cc_start: 0.8174 (m100) cc_final: 0.7585 (m100) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1563 time to fit residues: 18.6014 Evaluate side-chains 80 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 HIS ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4772 Z= 0.215 Angle : 0.665 7.698 6486 Z= 0.334 Chirality : 0.045 0.302 727 Planarity : 0.004 0.046 825 Dihedral : 7.928 82.299 667 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 24.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.14 (0.34), residues: 577 helix: -1.77 (0.97), residues: 23 sheet: -0.52 (0.32), residues: 233 loop : -0.79 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.006 TRP D 162 HIS 0.004 0.001 HIS C 210 PHE 0.015 0.002 PHE D 74 TYR 0.013 0.002 TYR C 113 ARG 0.005 0.000 ARG C 363 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 40 VAL cc_start: 0.9336 (t) cc_final: 0.9110 (p) REVERT: C 233 ILE cc_start: 0.9339 (mp) cc_final: 0.9058 (mp) REVERT: C 272 TYR cc_start: 0.7741 (m-80) cc_final: 0.7271 (m-80) REVERT: C 327 LEU cc_start: 0.9675 (mt) cc_final: 0.9474 (mt) REVERT: C 352 MET cc_start: 0.8475 (ppp) cc_final: 0.8203 (ppp) REVERT: D 101 PHE cc_start: 0.9512 (m-80) cc_final: 0.8964 (m-80) REVERT: D 209 MET cc_start: 0.8749 (mpp) cc_final: 0.8374 (mpp) REVERT: D 229 TRP cc_start: 0.8113 (m100) cc_final: 0.7501 (m100) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1635 time to fit residues: 19.7022 Evaluate side-chains 80 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 HIS ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.075046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.059855 restraints weight = 20697.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.062011 restraints weight = 12780.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.063537 restraints weight = 9140.796| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 4772 Z= 0.397 Angle : 0.786 8.558 6486 Z= 0.403 Chirality : 0.045 0.150 727 Planarity : 0.005 0.046 825 Dihedral : 8.352 83.686 667 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 35.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.45 (0.34), residues: 577 helix: -1.97 (0.98), residues: 23 sheet: -0.88 (0.32), residues: 223 loop : -0.88 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.006 TRP D 236 HIS 0.008 0.002 HIS C 210 PHE 0.025 0.003 PHE D 74 TYR 0.016 0.003 TYR D 39 ARG 0.006 0.001 ARG C 363 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1204.37 seconds wall clock time: 22 minutes 50.03 seconds (1370.03 seconds total)