Starting phenix.real_space_refine on Tue Feb 13 08:15:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkm_27490/02_2024/8dkm_27490_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkm_27490/02_2024/8dkm_27490.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkm_27490/02_2024/8dkm_27490_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkm_27490/02_2024/8dkm_27490_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkm_27490/02_2024/8dkm_27490_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkm_27490/02_2024/8dkm_27490.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkm_27490/02_2024/8dkm_27490.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkm_27490/02_2024/8dkm_27490_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkm_27490/02_2024/8dkm_27490_updated.pdb" } resolution = 3.39 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= 0.004 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 2867 2.51 5 N 706 2.21 5 O 793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 55": "OE1" <-> "OE2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4383 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 876 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "B" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2693 Unusual residues: {'IYY': 1} Classifications: {'peptide': 334, 'undetermined': 1} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 15, 'TRANS': 318, None: 1} Not linked: pdbres="TYR P 357 " pdbres="IYY P 501 " Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 2.77, per 1000 atoms: 0.63 Number of scatterers: 4383 At special positions: 0 Unit cell: (85.884, 105.25, 106.092, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 793 8.00 N 706 7.00 C 2867 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " 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=0, symmetry=0 Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 824.3 milliseconds 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 9 sheets defined 34.2% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'P' and resid 121 through 149 removed outlier: 4.366A pdb=" N PHE P 142 " --> pdb=" O TRP P 138 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N TYR P 143 " --> pdb=" O SER P 139 " (cutoff:3.500A) Proline residue: P 144 - end of helix Processing helix chain 'P' and resid 160 through 180 removed outlier: 3.799A pdb=" N LEU P 180 " --> pdb=" O PHE P 176 " (cutoff:3.500A) Processing helix chain 'P' and resid 184 through 193 Processing helix chain 'P' and resid 203 through 225 Processing helix chain 'P' and resid 235 through 256 Processing helix chain 'P' and resid 262 through 279 removed outlier: 3.963A pdb=" N PHE P 269 " --> pdb=" O PHE P 265 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER P 270 " --> pdb=" O LEU P 266 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL P 276 " --> pdb=" O ILE P 272 " (cutoff:3.500A) Processing helix chain 'P' and resid 282 through 291 Processing helix chain 'P' and resid 299 through 322 Processing helix chain 'P' and resid 326 through 329 No H-bonds generated for 'chain 'P' and resid 326 through 329' Processing helix chain 'P' and resid 333 through 354 removed outlier: 4.634A pdb=" N LEU P 338 " --> pdb=" O THR P 334 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 5 through 7 Processing sheet with id= B, first strand: chain 'A' and resid 94 through 98 removed outlier: 6.053A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.405A pdb=" N LYS B 103 " --> pdb=" O LEU B 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 19 through 22 Processing sheet with id= E, first strand: chain 'B' and resid 84 through 90 removed outlier: 6.072A pdb=" N GLN B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LYS B 39 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'P' and resid 31 through 35 removed outlier: 6.360A pdb=" N ARG P 114 " --> pdb=" O VAL P 32 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU P 34 " --> pdb=" O ARG P 114 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU P 116 " --> pdb=" O LEU P 34 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'P' and resid 39 through 44 Processing sheet with id= H, first strand: chain 'P' and resid 54 through 56 Processing sheet with id= I, first strand: chain 'P' and resid 57 through 62 removed outlier: 3.776A pdb=" N THR P 57 " --> pdb=" O HIS P 102 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR P 98 " --> pdb=" O THR P 61 " (cutoff:3.500A) 189 hydrogen bonds defined for protein. 540 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: 1.30 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 1570 1.38 - 1.56: 2907 1.56 - 1.74: 0 1.74 - 1.92: 24 1.92 - 2.10: 1 Bond restraints: 4502 Sorted by residual: bond pdb=" C ASN P 301 " pdb=" O ASN P 301 " ideal model delta sigma weight residual 1.237 1.198 0.039 1.17e-02 7.31e+03 1.10e+01 bond pdb=" N ILE P 260 " pdb=" CA ILE P 260 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.18e-02 7.18e+03 9.88e+00 bond pdb=" N THR P 261 " pdb=" CA THR P 261 " ideal model delta sigma weight residual 1.452 1.488 -0.035 1.25e-02 6.40e+03 7.98e+00 bond pdb=" CA VAL P 302 " pdb=" CB VAL P 302 " ideal model delta sigma weight residual 1.540 1.501 0.038 1.37e-02 5.33e+03 7.81e+00 bond pdb=" N VAL P 259 " pdb=" CA VAL P 259 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.42e-02 4.96e+03 5.60e+00 ... (remaining 4497 not shown) Histogram of bond angle deviations from ideal: 99.29 - 106.27: 112 106.27 - 113.24: 2405 113.24 - 120.21: 1576 120.21 - 127.18: 1991 127.18 - 134.15: 54 Bond angle restraints: 6138 Sorted by residual: angle pdb=" N GLY P 300 " pdb=" CA GLY P 300 " pdb=" C GLY P 300 " ideal model delta sigma weight residual 113.37 105.91 7.46 1.34e+00 5.57e-01 3.10e+01 angle pdb=" N TYR P 271 " pdb=" CA TYR P 271 " pdb=" C TYR P 271 " ideal model delta sigma weight residual 111.36 115.75 -4.39 1.09e+00 8.42e-01 1.62e+01 angle pdb=" N VAL P 259 " pdb=" CA VAL P 259 " pdb=" C VAL P 259 " ideal model delta sigma weight residual 111.45 107.73 3.72 9.30e-01 1.16e+00 1.60e+01 angle pdb=" C PRO A 62 " pdb=" N ASP A 63 " pdb=" CA ASP A 63 " ideal model delta sigma weight residual 121.54 128.03 -6.49 1.91e+00 2.74e-01 1.16e+01 angle pdb=" CA THR P 261 " pdb=" C THR P 261 " pdb=" O THR P 261 " ideal model delta sigma weight residual 121.82 118.01 3.81 1.21e+00 6.83e-01 9.94e+00 ... (remaining 6133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.19: 2275 15.19 - 30.38: 250 30.38 - 45.57: 49 45.57 - 60.76: 7 60.76 - 75.94: 4 Dihedral angle restraints: 2585 sinusoidal: 988 harmonic: 1597 Sorted by residual: dihedral pdb=" CA SER P 270 " pdb=" C SER P 270 " pdb=" N TYR P 271 " pdb=" CA TYR P 271 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 88 " pdb=" CB CYS B 88 " ideal model delta sinusoidal sigma weight residual 93.00 61.96 31.04 1 1.00e+01 1.00e-02 1.37e+01 dihedral pdb=" CA ARG P 47 " pdb=" C ARG P 47 " pdb=" N PRO P 48 " pdb=" CA PRO P 48 " ideal model delta harmonic sigma weight residual 180.00 163.67 16.33 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 2582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 547 0.050 - 0.100: 118 0.100 - 0.150: 26 0.150 - 0.200: 3 0.200 - 0.250: 1 Chirality restraints: 695 Sorted by residual: chirality pdb=" CA TYR P 271 " pdb=" N TYR P 271 " pdb=" C TYR P 271 " pdb=" CB TYR P 271 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA VAL P 259 " pdb=" N VAL P 259 " pdb=" C VAL P 259 " pdb=" CB VAL P 259 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.39e-01 chirality pdb=" CB VAL P 279 " pdb=" CA VAL P 279 " pdb=" CG1 VAL P 279 " pdb=" CG2 VAL P 279 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.88e-01 ... (remaining 692 not shown) Planarity restraints: 767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN P 199 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO P 200 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO P 200 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO P 200 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP P 182 " -0.014 2.00e-02 2.50e+03 1.10e-02 3.02e+00 pdb=" CG TRP P 182 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP P 182 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP P 182 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP P 182 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP P 182 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP P 182 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 182 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 182 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP P 182 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP P 235 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO P 236 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO P 236 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO P 236 " 0.021 5.00e-02 4.00e+02 ... (remaining 764 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 800 2.77 - 3.30: 4124 3.30 - 3.84: 7057 3.84 - 4.37: 8012 4.37 - 4.90: 14364 Nonbonded interactions: 34357 Sorted by model distance: nonbonded pdb=" O SER A 52 " pdb=" NH1 ARG A 73 " model vdw 2.241 2.520 nonbonded pdb=" OG1 THR A 40 " pdb=" O GLU A 42 " model vdw 2.245 2.440 nonbonded pdb=" O PHE A 29 " pdb=" NH2 ARG A 73 " model vdw 2.265 2.520 nonbonded pdb=" OD1 ASP B 42 " pdb=" N ILE B 43 " model vdw 2.277 2.520 nonbonded pdb=" OD1 ASP P 161 " pdb=" N PHE P 162 " model vdw 2.285 2.520 ... (remaining 34352 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: 1.270 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: 5.680 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.100 Find NCS groups from input model: 0.120 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 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 : 0.003 0.039 4502 Z= 0.212 Angle : 0.640 7.461 6138 Z= 0.350 Chirality : 0.045 0.250 695 Planarity : 0.005 0.068 767 Dihedral : 12.928 75.945 1559 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.83 % Allowed : 0.41 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.94 (0.37), residues: 547 helix: 1.16 (0.39), residues: 198 sheet: -0.77 (0.48), residues: 131 loop : -2.24 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP P 182 HIS 0.002 0.001 HIS P 211 PHE 0.017 0.001 PHE P 289 TYR 0.015 0.001 TYR P 286 ARG 0.008 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.417 Fit side-chains REVERT: A 83 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7269 (tp-100) REVERT: B 81 GLU cc_start: 0.7038 (mp0) cc_final: 0.6829 (mp0) outliers start: 4 outliers final: 2 residues processed: 83 average time/residue: 0.1427 time to fit residues: 15.6318 Evaluate side-chains 70 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 272 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 0.0770 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN P 149 ASN P 301 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.0608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4502 Z= 0.164 Angle : 0.543 6.814 6138 Z= 0.275 Chirality : 0.042 0.137 695 Planarity : 0.004 0.041 767 Dihedral : 4.872 37.301 607 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.07 % Allowed : 9.75 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.65 (0.37), residues: 547 helix: 1.34 (0.38), residues: 201 sheet: -0.69 (0.48), residues: 131 loop : -2.00 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP P 182 HIS 0.002 0.000 HIS B 55 PHE 0.021 0.001 PHE P 289 TYR 0.021 0.001 TYR P 134 ARG 0.005 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.468 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 34 MET cc_start: 0.8878 (mmm) cc_final: 0.8449 (mmm) REVERT: B 81 GLU cc_start: 0.7047 (mp0) cc_final: 0.6841 (mp0) outliers start: 10 outliers final: 9 residues processed: 82 average time/residue: 0.1294 time to fit residues: 14.3572 Evaluate side-chains 81 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 149 ASN Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 252 MET Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4502 Z= 0.244 Angle : 0.575 7.292 6138 Z= 0.292 Chirality : 0.044 0.141 695 Planarity : 0.004 0.037 767 Dihedral : 4.827 42.045 602 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.11 % Allowed : 13.07 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.53 (0.38), residues: 547 helix: 1.51 (0.38), residues: 201 sheet: -0.74 (0.49), residues: 135 loop : -1.94 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 182 HIS 0.003 0.001 HIS B 55 PHE 0.012 0.001 PHE P 87 TYR 0.021 0.002 TYR P 134 ARG 0.004 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 0.469 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: B 81 GLU cc_start: 0.7107 (mp0) cc_final: 0.6896 (mp0) REVERT: P 189 GLN cc_start: 0.7726 (tm-30) cc_final: 0.7468 (tm-30) REVERT: P 222 GLN cc_start: 0.7561 (tt0) cc_final: 0.7324 (tt0) outliers start: 15 outliers final: 14 residues processed: 83 average time/residue: 0.1364 time to fit residues: 15.2065 Evaluate side-chains 89 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 196 ASN Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 252 MET Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 344 VAL Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 27 GLN P 149 ASN P 196 ASN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4502 Z= 0.189 Angle : 0.538 6.931 6138 Z= 0.276 Chirality : 0.043 0.136 695 Planarity : 0.004 0.037 767 Dihedral : 4.788 44.333 602 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.58 % Favored : 93.24 % Rotamer: Outliers : 4.15 % Allowed : 14.73 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.33 (0.38), residues: 547 helix: 1.87 (0.38), residues: 195 sheet: -0.80 (0.49), residues: 137 loop : -1.81 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 182 HIS 0.002 0.000 HIS B 55 PHE 0.021 0.001 PHE P 289 TYR 0.018 0.001 TYR P 134 ARG 0.005 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 75 time to evaluate : 0.497 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 83 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7380 (tp-100) REVERT: B 81 GLU cc_start: 0.7063 (mp0) cc_final: 0.6856 (mp0) outliers start: 20 outliers final: 16 residues processed: 85 average time/residue: 0.1215 time to fit residues: 14.2179 Evaluate side-chains 88 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 149 ASN Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 196 ASN Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 252 MET Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 44 optimal weight: 0.0670 chunk 36 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 17 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN P 149 ASN ** P 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4502 Z= 0.167 Angle : 0.540 6.538 6138 Z= 0.277 Chirality : 0.042 0.132 695 Planarity : 0.004 0.036 767 Dihedral : 4.775 45.762 602 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.40 % Favored : 93.42 % Rotamer: Outliers : 3.94 % Allowed : 14.32 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.26 (0.38), residues: 547 helix: 1.75 (0.38), residues: 200 sheet: -0.66 (0.48), residues: 140 loop : -1.74 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 182 HIS 0.001 0.000 HIS B 55 PHE 0.010 0.001 PHE P 345 TYR 0.017 0.001 TYR P 134 ARG 0.006 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 73 time to evaluate : 0.519 Fit side-chains REVERT: B 81 GLU cc_start: 0.7041 (mp0) cc_final: 0.6824 (mp0) outliers start: 19 outliers final: 16 residues processed: 80 average time/residue: 0.1276 time to fit residues: 14.0504 Evaluate side-chains 88 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 247 PHE Chi-restraints excluded: chain P residue 252 MET Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 5 optimal weight: 0.0470 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 27 GLN ** P 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4502 Z= 0.205 Angle : 0.555 6.780 6138 Z= 0.284 Chirality : 0.043 0.133 695 Planarity : 0.004 0.036 767 Dihedral : 4.853 46.940 602 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.40 % Favored : 93.42 % Rotamer: Outliers : 3.94 % Allowed : 15.56 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.21 (0.38), residues: 547 helix: 1.92 (0.38), residues: 195 sheet: -0.73 (0.48), residues: 142 loop : -1.70 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 182 HIS 0.002 0.001 HIS B 55 PHE 0.022 0.001 PHE P 289 TYR 0.018 0.001 TYR P 134 ARG 0.006 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 73 time to evaluate : 0.496 Fit side-chains REVERT: A 83 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7406 (tp-100) REVERT: B 81 GLU cc_start: 0.7079 (mp0) cc_final: 0.6869 (mp0) outliers start: 19 outliers final: 17 residues processed: 80 average time/residue: 0.1169 time to fit residues: 12.9446 Evaluate side-chains 89 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 71 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 217 LEU Chi-restraints excluded: chain P residue 252 MET Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 27 GLN P 196 ASN ** P 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4502 Z= 0.234 Angle : 0.569 7.027 6138 Z= 0.291 Chirality : 0.043 0.134 695 Planarity : 0.004 0.036 767 Dihedral : 4.933 47.158 602 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 4.36 % Allowed : 15.56 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.22 (0.38), residues: 547 helix: 1.90 (0.38), residues: 195 sheet: -0.71 (0.48), residues: 142 loop : -1.73 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 182 HIS 0.002 0.001 HIS B 55 PHE 0.012 0.001 PHE P 87 TYR 0.020 0.001 TYR P 134 ARG 0.007 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 72 time to evaluate : 0.491 Fit side-chains REVERT: A 18 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8464 (tt) REVERT: A 83 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7351 (tp-100) REVERT: B 81 GLU cc_start: 0.7104 (mp0) cc_final: 0.6898 (mp0) outliers start: 21 outliers final: 18 residues processed: 81 average time/residue: 0.1247 time to fit residues: 13.7945 Evaluate side-chains 92 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 196 ASN Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 217 LEU Chi-restraints excluded: chain P residue 252 MET Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 27 GLN ** P 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4502 Z= 0.215 Angle : 0.565 6.989 6138 Z= 0.287 Chirality : 0.043 0.133 695 Planarity : 0.004 0.036 767 Dihedral : 4.940 47.312 602 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.73 % Allowed : 17.43 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.21 (0.38), residues: 547 helix: 1.93 (0.38), residues: 195 sheet: -0.72 (0.48), residues: 142 loop : -1.72 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 182 HIS 0.002 0.001 HIS B 55 PHE 0.023 0.001 PHE P 289 TYR 0.019 0.001 TYR P 134 ARG 0.006 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 0.551 Fit side-chains REVERT: A 83 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7421 (tp-100) REVERT: B 81 GLU cc_start: 0.7114 (mp0) cc_final: 0.6911 (mp0) outliers start: 18 outliers final: 17 residues processed: 79 average time/residue: 0.1253 time to fit residues: 13.5431 Evaluate side-chains 89 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 71 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 217 LEU Chi-restraints excluded: chain P residue 252 MET Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 51 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 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 83 GLN B 27 GLN P 222 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4502 Z= 0.205 Angle : 0.564 6.914 6138 Z= 0.286 Chirality : 0.043 0.131 695 Planarity : 0.004 0.041 767 Dihedral : 4.929 47.533 602 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 4.15 % Allowed : 17.01 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.21 (0.38), residues: 547 helix: 1.99 (0.38), residues: 194 sheet: -0.74 (0.48), residues: 142 loop : -1.75 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 182 HIS 0.002 0.001 HIS B 55 PHE 0.011 0.001 PHE P 87 TYR 0.019 0.001 TYR P 134 ARG 0.008 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 0.507 Fit side-chains REVERT: A 83 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7477 (tp-100) REVERT: B 24 ARG cc_start: 0.7679 (mtp-110) cc_final: 0.7427 (mtp-110) REVERT: B 81 GLU cc_start: 0.7106 (mp0) cc_final: 0.6902 (mp0) outliers start: 20 outliers final: 18 residues processed: 79 average time/residue: 0.1173 time to fit residues: 12.8362 Evaluate side-chains 90 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 71 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 217 LEU Chi-restraints excluded: chain P residue 252 MET Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 344 VAL Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 0.0980 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 27 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4502 Z= 0.183 Angle : 0.557 6.712 6138 Z= 0.284 Chirality : 0.042 0.129 695 Planarity : 0.004 0.039 767 Dihedral : 4.889 47.747 602 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 4.15 % Allowed : 17.01 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.17 (0.39), residues: 547 helix: 2.01 (0.38), residues: 194 sheet: -0.71 (0.49), residues: 142 loop : -1.73 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 182 HIS 0.001 0.000 HIS B 55 PHE 0.024 0.001 PHE P 289 TYR 0.018 0.001 TYR P 134 ARG 0.008 0.000 ARG B 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 0.484 Fit side-chains REVERT: A 18 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8428 (tt) REVERT: A 83 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7370 (tp-100) REVERT: B 24 ARG cc_start: 0.7653 (mtp-110) cc_final: 0.7385 (mtp-110) REVERT: B 81 GLU cc_start: 0.7092 (mp0) cc_final: 0.6888 (mp0) outliers start: 20 outliers final: 18 residues processed: 79 average time/residue: 0.1191 time to fit residues: 12.9298 Evaluate side-chains 91 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 71 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 217 LEU Chi-restraints excluded: chain P residue 252 MET Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 344 VAL Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.0270 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 27 GLN P 96 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.154438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.124137 restraints weight = 5488.728| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.18 r_work: 0.3189 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4502 Z= 0.157 Angle : 0.542 6.490 6138 Z= 0.275 Chirality : 0.042 0.127 695 Planarity : 0.004 0.037 767 Dihedral : 4.818 48.021 602 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.94 % Allowed : 18.05 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.16 (0.39), residues: 547 helix: 1.81 (0.38), residues: 201 sheet: -0.61 (0.49), residues: 140 loop : -1.68 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 182 HIS 0.001 0.000 HIS B 55 PHE 0.010 0.001 PHE P 345 TYR 0.022 0.001 TYR P 271 ARG 0.008 0.000 ARG B 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1260.35 seconds wall clock time: 23 minutes 27.37 seconds (1407.37 seconds total)