Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 00:11:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkm_27490/10_2023/8dkm_27490_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkm_27490/10_2023/8dkm_27490.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkm_27490/10_2023/8dkm_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_27490/10_2023/8dkm_27490_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkm_27490/10_2023/8dkm_27490_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkm_27490/10_2023/8dkm_27490.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkm_27490/10_2023/8dkm_27490.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkm_27490/10_2023/8dkm_27490_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkm_27490/10_2023/8dkm_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 2.93, per 1000 atoms: 0.67 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: 2.00 Conformation dependent library (CDL) restraints added in 640.8 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: 0.81 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: 1.05 Time building geometry restraints manager: 2.02 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: 2273 15.19 - 30.38: 250 30.38 - 45.57: 47 45.57 - 60.76: 7 60.76 - 75.94: 4 Dihedral angle restraints: 2581 sinusoidal: 984 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 2578 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: 1.550 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: 5.710 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.820 Find NCS groups from input model: 0.130 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.040 ------------------------------------------------------------------------------- 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 : 12.857 75.945 1555 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 *********************** 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 : 0.521 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 83 average time/residue: 0.1405 time to fit residues: 15.4190 Evaluate side-chains 69 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 0.474 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0458 time to fit residues: 0.8812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.8980 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: A 83 GLN B 27 GLN P 149 ASN P 301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.0651 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= 0.163 Angle : 0.544 6.808 6138 Z= 0.275 Chirality : 0.042 0.136 695 Planarity : 0.004 0.041 767 Dihedral : 4.091 16.246 596 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.87 % Allowed : 10.37 % Favored : 87.76 % 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: -0.65 (0.37), residues: 547 helix: 1.33 (0.38), residues: 201 sheet: -0.67 (0.48), residues: 131 loop : -1.99 (0.40), residues: 215 *********************** 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 86 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.470 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. outliers start: 9 outliers final: 8 residues processed: 81 average time/residue: 0.1285 time to fit residues: 14.0466 Evaluate side-chains 80 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.468 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0412 time to fit residues: 1.2349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.0938 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= 0.231 Angle : 0.572 7.273 6138 Z= 0.290 Chirality : 0.044 0.223 695 Planarity : 0.004 0.037 767 Dihedral : 4.244 17.482 596 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 1.87 % Allowed : 13.07 % Favored : 85.06 % 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: -0.50 (0.38), residues: 547 helix: 1.57 (0.38), residues: 201 sheet: -0.68 (0.49), residues: 131 loop : -1.99 (0.41), residues: 215 *********************** 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 85 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.525 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. outliers start: 9 outliers final: 7 residues processed: 81 average time/residue: 0.1361 time to fit residues: 14.9875 Evaluate side-chains 80 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.513 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0515 time to fit residues: 1.3053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 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 0.035 4502 Z= 0.206 Angle : 0.550 7.206 6138 Z= 0.282 Chirality : 0.043 0.137 695 Planarity : 0.004 0.037 767 Dihedral : 4.233 17.163 596 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.76 % Favored : 93.05 % Rotamer: Outliers : 2.70 % Allowed : 14.52 % Favored : 82.78 % 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: -0.38 (0.38), residues: 547 helix: 1.84 (0.38), residues: 195 sheet: -0.76 (0.49), residues: 133 loop : -1.89 (0.41), residues: 219 *********************** 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 88 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.476 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. outliers start: 13 outliers final: 8 residues processed: 81 average time/residue: 0.1237 time to fit residues: 13.9932 Evaluate side-chains 80 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.494 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0498 time to fit residues: 1.3843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0370 chunk 21 optimal weight: 0.0470 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 0.0870 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 47 optimal weight: 0.0770 overall best weight: 0.1892 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4502 Z= 0.123 Angle : 0.522 6.067 6138 Z= 0.264 Chirality : 0.041 0.126 695 Planarity : 0.004 0.036 767 Dihedral : 3.975 15.973 596 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.04 % Allowed : 16.39 % Favored : 82.57 % 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: -0.20 (0.38), residues: 547 helix: 1.74 (0.38), residues: 201 sheet: -0.40 (0.50), residues: 129 loop : -1.79 (0.42), residues: 217 *********************** 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 81 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.440 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 79 average time/residue: 0.1543 time to fit residues: 15.8590 Evaluate side-chains 74 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 0.512 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0491 time to fit residues: 0.9683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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: 0.8158 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4502 Z= 0.253 Angle : 0.586 8.170 6138 Z= 0.299 Chirality : 0.044 0.137 695 Planarity : 0.004 0.036 767 Dihedral : 4.337 17.291 596 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.95 % Favored : 92.87 % Rotamer: Outliers : 2.07 % Allowed : 17.01 % Favored : 80.91 % 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: -0.27 (0.38), residues: 547 helix: 1.66 (0.38), residues: 201 sheet: -0.57 (0.48), residues: 136 loop : -1.75 (0.42), residues: 210 *********************** 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 87 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.520 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. outliers start: 10 outliers final: 8 residues processed: 79 average time/residue: 0.1394 time to fit residues: 14.6550 Evaluate side-chains 84 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.500 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0458 time to fit residues: 1.3279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 0.0000 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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: 0.8128 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4502 Z= 0.190 Angle : 0.569 9.866 6138 Z= 0.287 Chirality : 0.042 0.131 695 Planarity : 0.004 0.036 767 Dihedral : 4.262 17.107 596 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.24 % Allowed : 17.01 % 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: -0.19 (0.38), residues: 547 helix: 1.94 (0.38), residues: 194 sheet: -0.65 (0.48), residues: 138 loop : -1.73 (0.42), residues: 215 *********************** 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 79 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.513 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 74 average time/residue: 0.1319 time to fit residues: 13.2804 Evaluate side-chains 74 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 0.516 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0554 time to fit residues: 0.8740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 38 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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: 0.8126 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4502 Z= 0.187 Angle : 0.557 8.930 6138 Z= 0.280 Chirality : 0.042 0.132 695 Planarity : 0.004 0.036 767 Dihedral : 4.221 16.831 596 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.24 % Allowed : 18.67 % 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: -0.18 (0.38), residues: 547 helix: 1.94 (0.38), residues: 195 sheet: -0.66 (0.48), residues: 138 loop : -1.71 (0.42), residues: 214 *********************** 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 78 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.469 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 74 average time/residue: 0.1330 time to fit residues: 13.2159 Evaluate side-chains 73 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.514 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0429 time to fit residues: 0.8070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 45 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1536 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= 0.214 Angle : 0.575 9.054 6138 Z= 0.290 Chirality : 0.043 0.133 695 Planarity : 0.004 0.037 767 Dihedral : 4.285 18.379 596 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.04 % Allowed : 19.92 % Favored : 79.05 % 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: -0.19 (0.38), residues: 547 helix: 1.94 (0.38), residues: 194 sheet: -0.63 (0.49), residues: 138 loop : -1.74 (0.42), residues: 215 *********************** 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 77 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.494 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 73 average time/residue: 0.1407 time to fit residues: 13.8577 Evaluate side-chains 77 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 0.499 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0579 time to fit residues: 1.0560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 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 79 ASN A 83 GLN B 27 GLN P 196 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4502 Z= 0.187 Angle : 0.559 8.663 6138 Z= 0.283 Chirality : 0.042 0.131 695 Planarity : 0.004 0.041 767 Dihedral : 4.251 17.909 596 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.62 % Allowed : 19.92 % Favored : 79.46 % 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 (0.38), residues: 547 helix: 1.92 (0.38), residues: 195 sheet: -0.58 (0.49), residues: 138 loop : -1.71 (0.42), residues: 214 ********************** 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 73 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.532 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 73 average time/residue: 0.1304 time to fit residues: 13.0028 Evaluate side-chains 72 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 0.463 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0451 time to fit residues: 0.8327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 83 GLN B 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.152668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.122578 restraints weight = 5454.753| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.11 r_work: 0.3169 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4502 Z= 0.223 Angle : 0.583 8.954 6138 Z= 0.294 Chirality : 0.043 0.134 695 Planarity : 0.004 0.042 767 Dihedral : 4.310 18.077 596 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.83 % Allowed : 20.95 % Favored : 78.22 % 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: -0.18 (0.38), residues: 547 helix: 1.92 (0.38), residues: 195 sheet: -0.58 (0.49), residues: 138 loop : -1.74 (0.42), residues: 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1335.39 seconds wall clock time: 24 minutes 40.90 seconds (1480.90 seconds total)