Starting phenix.real_space_refine on Sun Mar 10 16:18:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbv_34644/03_2024/8hbv_34644_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbv_34644/03_2024/8hbv_34644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbv_34644/03_2024/8hbv_34644.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbv_34644/03_2024/8hbv_34644.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbv_34644/03_2024/8hbv_34644_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbv_34644/03_2024/8hbv_34644_updated.pdb" } resolution = 2.51 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= 0.005 sd= 0.118 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 4 5.49 5 S 18 5.16 5 C 2100 2.51 5 N 543 2.21 5 O 614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "B GLU 6": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3279 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2180 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 274} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 997 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 102 Unusual residues: {'CDL': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 102 Time building chain proxies: 2.76, per 1000 atoms: 0.84 Number of scatterers: 3279 At special positions: 0 Unit cell: (69.222, 68.388, 110.922, 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 18 16.00 P 4 15.00 O 614 8.00 N 543 7.00 C 2100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.02 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: 1.31 Conformation dependent library (CDL) restraints added in 769.3 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 754 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 13 helices and 4 sheets defined 54.3% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 12 through 41 Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 57 through 68 Processing helix chain 'A' and resid 77 through 104 removed outlier: 4.567A pdb=" N ASP A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N THR A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 142 Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 156 through 167 Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 176 through 203 Processing helix chain 'A' and resid 211 through 241 Proline residue: A 231 - end of helix Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 270 through 297 Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 3 through 7 Processing sheet with id= B, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.162A pdb=" N THR B 118 " --> pdb=" O VAL B 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 115 through 117 removed outlier: 6.008A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 97 through 100 204 hydrogen bonds defined for protein. 588 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: 0.88 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 743 1.33 - 1.45: 730 1.45 - 1.57: 1842 1.57 - 1.69: 8 1.69 - 1.81: 27 Bond restraints: 3350 Sorted by residual: bond pdb=" CA7 CDL A 401 " pdb=" OA8 CDL A 401 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.21e+02 bond pdb=" CB7 CDL A 401 " pdb=" OB8 CDL A 401 " ideal model delta sigma weight residual 1.334 1.443 -0.109 1.10e-02 8.26e+03 9.87e+01 bond pdb=" CA5 CDL A 401 " pdb=" OA6 CDL A 401 " ideal model delta sigma weight residual 1.342 1.453 -0.111 1.50e-02 4.44e+03 5.50e+01 bond pdb=" CB5 CDL A 401 " pdb=" OB6 CDL A 401 " ideal model delta sigma weight residual 1.342 1.446 -0.104 1.50e-02 4.44e+03 4.82e+01 bond pdb=" C21 PC1 A 402 " pdb=" O21 PC1 A 402 " ideal model delta sigma weight residual 1.331 1.455 -0.124 2.00e-02 2.50e+03 3.85e+01 ... (remaining 3345 not shown) Histogram of bond angle deviations from ideal: 97.10 - 104.48: 56 104.48 - 111.86: 1672 111.86 - 119.24: 1066 119.24 - 126.62: 1689 126.62 - 134.00: 58 Bond angle restraints: 4541 Sorted by residual: angle pdb=" C51 CDL A 401 " pdb=" CB5 CDL A 401 " pdb=" OB6 CDL A 401 " ideal model delta sigma weight residual 111.33 120.29 -8.96 1.32e+00 5.72e-01 4.60e+01 angle pdb=" C11 CDL A 401 " pdb=" CA5 CDL A 401 " pdb=" OA6 CDL A 401 " ideal model delta sigma weight residual 111.33 120.24 -8.91 1.32e+00 5.72e-01 4.54e+01 angle pdb=" C71 CDL A 401 " pdb=" CB7 CDL A 401 " pdb=" OB8 CDL A 401 " ideal model delta sigma weight residual 111.64 122.46 -10.82 1.65e+00 3.69e-01 4.32e+01 angle pdb=" C31 CDL A 401 " pdb=" CA7 CDL A 401 " pdb=" OA8 CDL A 401 " ideal model delta sigma weight residual 111.64 121.14 -9.50 1.65e+00 3.69e-01 3.33e+01 angle pdb=" OB8 CDL A 401 " pdb=" CB7 CDL A 401 " pdb=" OB9 CDL A 401 " ideal model delta sigma weight residual 123.94 117.51 6.43 1.21e+00 6.80e-01 2.81e+01 ... (remaining 4536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.33: 1803 19.33 - 38.67: 147 38.67 - 58.00: 41 58.00 - 77.33: 4 77.33 - 96.66: 4 Dihedral angle restraints: 1999 sinusoidal: 816 harmonic: 1183 Sorted by residual: dihedral pdb=" CA ALA A 208 " pdb=" C ALA A 208 " pdb=" N ASP A 209 " pdb=" CA ASP A 209 " ideal model delta harmonic sigma weight residual -180.00 -161.91 -18.09 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA5 CDL A 401 " pdb=" CA4 CDL A 401 " pdb=" OA6 CDL A 401 " pdb=" CA6 CDL A 401 " ideal model delta sinusoidal sigma weight residual 168.24 71.58 96.66 1 3.00e+01 1.11e-03 1.19e+01 dihedral pdb=" CA TRP B 111 " pdb=" C TRP B 111 " pdb=" N GLY B 112 " pdb=" CA GLY B 112 " ideal model delta harmonic sigma weight residual 180.00 163.81 16.19 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 1996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 237 0.030 - 0.059: 166 0.059 - 0.089: 64 0.089 - 0.118: 30 0.118 - 0.148: 9 Chirality restraints: 506 Sorted by residual: chirality pdb=" CA THR A 177 " pdb=" N THR A 177 " pdb=" C THR A 177 " pdb=" CB THR A 177 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA GLU A 167 " pdb=" N GLU A 167 " pdb=" C GLU A 167 " pdb=" CB GLU A 167 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA ARG A 276 " pdb=" N ARG A 276 " pdb=" C ARG A 276 " pdb=" CB ARG A 276 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 503 not shown) Planarity restraints: 566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 101 " 0.022 2.00e-02 2.50e+03 3.04e-02 1.61e+01 pdb=" CG PHE B 101 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 PHE B 101 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE B 101 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE B 101 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 101 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 101 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 211 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO A 212 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 9 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO A 10 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 10 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 10 " -0.020 5.00e-02 4.00e+02 ... (remaining 563 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 455 2.75 - 3.29: 3140 3.29 - 3.82: 5851 3.82 - 4.36: 6970 4.36 - 4.90: 11855 Nonbonded interactions: 28271 Sorted by model distance: nonbonded pdb=" OE2 GLU A 68 " pdb=" OG SER A 144 " model vdw 2.209 2.440 nonbonded pdb=" O VAL A 14 " pdb=" OG SER A 18 " model vdw 2.272 2.440 nonbonded pdb=" O TRP A 173 " pdb=" OG1 THR A 176 " model vdw 2.283 2.440 nonbonded pdb=" NH1 ARG A 238 " pdb=" OE2 GLU A 261 " model vdw 2.290 2.520 nonbonded pdb=" OD2 ASP B 100 " pdb=" NH1 ARG B 104 " model vdw 2.308 2.520 ... (remaining 28266 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 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: 1.330 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: 4.730 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.830 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 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 : 0.009 0.124 3350 Z= 0.624 Angle : 0.961 10.821 4541 Z= 0.500 Chirality : 0.048 0.148 506 Planarity : 0.005 0.052 566 Dihedral : 15.839 96.659 1242 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: 1.54 (0.38), residues: 410 helix: 1.88 (0.31), residues: 219 sheet: -0.75 (0.62), residues: 52 loop : 0.50 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 173 HIS 0.002 0.001 HIS A 9 PHE 0.069 0.004 PHE B 101 TYR 0.016 0.002 TYR A 157 ARG 0.005 0.001 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.412 Fit side-chains REVERT: A 70 ARG cc_start: 0.7215 (mtt180) cc_final: 0.6688 (ptt90) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 1.6209 time to fit residues: 110.9611 Evaluate side-chains 61 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3350 Z= 0.236 Angle : 0.533 5.504 4541 Z= 0.273 Chirality : 0.041 0.141 506 Planarity : 0.005 0.058 566 Dihedral : 12.968 71.643 535 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.07 % Allowed : 10.06 % Favored : 87.87 % 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: 2.15 (0.40), residues: 410 helix: 2.45 (0.32), residues: 219 sheet: -0.81 (0.62), residues: 54 loop : 0.83 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 57 HIS 0.001 0.000 HIS A 147 PHE 0.023 0.002 PHE A 17 TYR 0.013 0.001 TYR A 157 ARG 0.003 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.382 Fit side-chains REVERT: A 70 ARG cc_start: 0.7196 (mtt180) cc_final: 0.6771 (ptt90) REVERT: A 117 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6976 (mm) REVERT: A 228 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8172 (ttm) REVERT: B 89 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7273 (pt0) REVERT: B 106 GLU cc_start: 0.7429 (mp0) cc_final: 0.7195 (pm20) outliers start: 7 outliers final: 1 residues processed: 71 average time/residue: 1.5895 time to fit residues: 115.2826 Evaluate side-chains 68 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 89 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 0.0170 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3350 Z= 0.202 Angle : 0.490 5.449 4541 Z= 0.253 Chirality : 0.040 0.138 506 Planarity : 0.005 0.056 566 Dihedral : 11.873 58.508 535 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.14 % Allowed : 12.13 % Favored : 83.73 % 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: 2.37 (0.40), residues: 410 helix: 2.65 (0.32), residues: 219 sheet: -0.69 (0.64), residues: 54 loop : 0.88 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 57 HIS 0.001 0.000 HIS B 124 PHE 0.013 0.001 PHE B 101 TYR 0.013 0.001 TYR A 157 ARG 0.002 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 66 time to evaluate : 0.440 Fit side-chains REVERT: A 70 ARG cc_start: 0.7206 (mtt180) cc_final: 0.6786 (ptt90) REVERT: A 117 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6946 (mm) REVERT: B 89 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7291 (pt0) outliers start: 14 outliers final: 4 residues processed: 69 average time/residue: 1.5820 time to fit residues: 111.6242 Evaluate side-chains 73 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 89 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3350 Z= 0.223 Angle : 0.498 5.453 4541 Z= 0.256 Chirality : 0.040 0.136 506 Planarity : 0.005 0.055 566 Dihedral : 11.728 58.447 535 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.07 % Allowed : 15.09 % Favored : 82.84 % 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: 2.33 (0.40), residues: 410 helix: 2.57 (0.32), residues: 219 sheet: -0.64 (0.63), residues: 54 loop : 0.92 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 57 HIS 0.002 0.000 HIS B 59 PHE 0.014 0.002 PHE A 17 TYR 0.015 0.001 TYR A 157 ARG 0.003 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.373 Fit side-chains REVERT: A 70 ARG cc_start: 0.7183 (mtt180) cc_final: 0.6783 (ptt90) outliers start: 7 outliers final: 4 residues processed: 67 average time/residue: 1.6859 time to fit residues: 115.2716 Evaluate side-chains 68 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 53 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 0.0570 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3350 Z= 0.197 Angle : 0.476 5.431 4541 Z= 0.245 Chirality : 0.039 0.133 506 Planarity : 0.005 0.049 566 Dihedral : 11.389 57.778 535 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.66 % Allowed : 15.38 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.40), residues: 410 helix: 2.67 (0.32), residues: 219 sheet: -0.55 (0.64), residues: 54 loop : 0.98 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 57 HIS 0.001 0.000 HIS B 59 PHE 0.008 0.001 PHE A 128 TYR 0.014 0.001 TYR A 157 ARG 0.004 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.342 Fit side-chains REVERT: A 70 ARG cc_start: 0.7166 (mtt180) cc_final: 0.6786 (ptt90) outliers start: 9 outliers final: 4 residues processed: 69 average time/residue: 1.5989 time to fit residues: 112.6618 Evaluate side-chains 69 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 53 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS B 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3350 Z= 0.215 Angle : 0.485 5.434 4541 Z= 0.249 Chirality : 0.039 0.133 506 Planarity : 0.005 0.048 566 Dihedral : 11.354 57.052 535 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.25 % Allowed : 15.68 % Favored : 81.07 % 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: 2.45 (0.40), residues: 410 helix: 2.66 (0.32), residues: 219 sheet: -0.52 (0.64), residues: 54 loop : 0.96 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 57 HIS 0.001 0.001 HIS B 124 PHE 0.014 0.001 PHE A 17 TYR 0.014 0.001 TYR A 157 ARG 0.004 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.348 Fit side-chains REVERT: A 70 ARG cc_start: 0.7170 (mtt180) cc_final: 0.6797 (ptt90) outliers start: 11 outliers final: 6 residues processed: 71 average time/residue: 1.6135 time to fit residues: 116.9963 Evaluate side-chains 72 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 106 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.0020 chunk 39 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3350 Z= 0.170 Angle : 0.462 5.407 4541 Z= 0.238 Chirality : 0.038 0.129 506 Planarity : 0.004 0.046 566 Dihedral : 10.941 59.597 535 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.37 % Allowed : 16.27 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.40), residues: 410 helix: 2.79 (0.32), residues: 219 sheet: -0.41 (0.64), residues: 54 loop : 0.98 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 57 HIS 0.001 0.000 HIS B 124 PHE 0.010 0.001 PHE B 27 TYR 0.012 0.001 TYR A 157 ARG 0.005 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.439 Fit side-chains REVERT: A 70 ARG cc_start: 0.7197 (mtt180) cc_final: 0.6834 (ptt90) outliers start: 8 outliers final: 5 residues processed: 71 average time/residue: 1.5958 time to fit residues: 115.7463 Evaluate side-chains 70 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 106 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.0870 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3350 Z= 0.180 Angle : 0.467 5.407 4541 Z= 0.240 Chirality : 0.039 0.129 506 Planarity : 0.004 0.045 566 Dihedral : 10.835 59.505 535 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.07 % Allowed : 17.16 % Favored : 80.77 % 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: 2.62 (0.40), residues: 410 helix: 2.80 (0.32), residues: 219 sheet: -0.32 (0.65), residues: 54 loop : 0.99 (0.52), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 57 HIS 0.001 0.000 HIS B 59 PHE 0.008 0.001 PHE A 128 TYR 0.012 0.001 TYR A 157 ARG 0.006 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.389 Fit side-chains REVERT: A 70 ARG cc_start: 0.7184 (mtt180) cc_final: 0.6817 (ptt90) outliers start: 7 outliers final: 5 residues processed: 69 average time/residue: 1.6285 time to fit residues: 114.7894 Evaluate side-chains 70 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 106 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 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 214 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 3350 Z= 0.214 Angle : 0.476 5.399 4541 Z= 0.248 Chirality : 0.039 0.129 506 Planarity : 0.005 0.045 566 Dihedral : 10.694 59.519 535 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.48 % Allowed : 18.05 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.40), residues: 410 helix: 2.73 (0.32), residues: 220 sheet: -0.37 (0.64), residues: 54 loop : 1.01 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 57 HIS 0.001 0.000 HIS B 59 PHE 0.013 0.001 PHE A 17 TYR 0.012 0.001 TYR A 157 ARG 0.006 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.406 Fit side-chains REVERT: A 17 PHE cc_start: 0.7189 (t80) cc_final: 0.6715 (t80) REVERT: A 70 ARG cc_start: 0.7185 (mtt180) cc_final: 0.6822 (ptt90) REVERT: B 106 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7218 (pm20) outliers start: 5 outliers final: 4 residues processed: 68 average time/residue: 1.6737 time to fit residues: 116.2493 Evaluate side-chains 70 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 106 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 33 optimal weight: 0.0470 chunk 6 optimal weight: 0.3980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3350 Z= 0.169 Angle : 0.459 5.407 4541 Z= 0.239 Chirality : 0.038 0.128 506 Planarity : 0.004 0.044 566 Dihedral : 10.257 56.647 535 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.48 % Allowed : 18.34 % Favored : 80.18 % 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: 2.72 (0.40), residues: 410 helix: 2.88 (0.32), residues: 220 sheet: -0.29 (0.64), residues: 54 loop : 1.01 (0.52), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 57 HIS 0.001 0.000 HIS B 59 PHE 0.014 0.001 PHE A 17 TYR 0.010 0.001 TYR A 157 ARG 0.006 0.000 ARG A 293 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.386 Fit side-chains REVERT: A 17 PHE cc_start: 0.7155 (t80) cc_final: 0.6704 (t80) REVERT: A 70 ARG cc_start: 0.7198 (mtt180) cc_final: 0.6840 (ptt90) REVERT: B 106 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7209 (pm20) outliers start: 5 outliers final: 3 residues processed: 70 average time/residue: 1.7035 time to fit residues: 121.7442 Evaluate side-chains 70 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 106 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.133037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.112871 restraints weight = 3979.402| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.27 r_work: 0.3261 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 3350 Z= 0.224 Angle : 0.499 5.398 4541 Z= 0.259 Chirality : 0.039 0.129 506 Planarity : 0.005 0.044 566 Dihedral : 10.408 56.334 535 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.48 % Allowed : 18.64 % Favored : 79.88 % 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: 2.61 (0.40), residues: 410 helix: 2.78 (0.32), residues: 220 sheet: -0.35 (0.65), residues: 54 loop : 1.00 (0.52), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 57 HIS 0.002 0.000 HIS B 59 PHE 0.015 0.002 PHE A 17 TYR 0.011 0.001 TYR A 157 ARG 0.007 0.000 ARG A 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2339.61 seconds wall clock time: 41 minutes 48.84 seconds (2508.84 seconds total)