Starting phenix.real_space_refine on Sun May 19 16:30:35 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8ckz_16707.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8ckz_16707.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global+local_grid_search+nqh_flips resolution=3.07 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8ckz_16707.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8ckz_16707.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8ckz_16707.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8ckz_16707.pdb" } resolution = 3.07 refinement { run = *minimization_global rigid_body *local_grid_search morphing \ simulated_annealing adp occupancy *nqh_flips } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.019 sd= 0.164 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 18 5.16 5 C 1416 2.51 5 N 389 2.21 5 O 429 1.98 5 H 2261 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 4513 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3342 Inner-chain residues flagged as termini: ['pdbres="VAL A 86 "', 'pdbres="MET A 96 "'] Classifications: {'peptide': 212} Modifications used: {'COO': 2, 'NH2': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 197} Chain breaks: 1 Chain: "B" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1171 Classifications: {'peptide': 74} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 69} Time building chain proxies: 0.85, per 1000 atoms: 0.19 Number of scatterers: 4513 At special positions: 0 Unit cell: (70.68, 86.49, 99.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 O 429 8.00 N 389 7.00 C 1416 6.00 H 2261 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 137.4 milliseconds 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 538 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 1 sheets defined 64.7% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 17 through 29 Processing helix chain 'A' and resid 34 through 43 Proline residue: A 38 - end of helix Processing helix chain 'A' and resid 49 through 61 removed outlier: 4.006A pdb=" N THR A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 59 " --> pdb=" O MET A 55 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY A 61 " --> pdb=" O ASN A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 83 Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 111 through 117 Processing helix chain 'A' and resid 126 through 144 Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 161 through 174 Processing helix chain 'A' and resid 179 through 192 removed outlier: 4.431A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 204 removed outlier: 3.733A pdb=" N ILE A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'B' and resid 161 through 175 Processing helix chain 'B' and resid 179 through 187 Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 196 through 205 removed outlier: 3.558A pdb=" N ILE B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 220 removed outlier: 5.023A pdb=" N GLY B 220 " --> pdb=" O THR B 216 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 2 through 4 109 hydrogen bonds defined for protein. 315 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.75 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 2257 1.15 - 1.31: 393 1.31 - 1.48: 868 1.48 - 1.65: 1007 1.65 - 1.81: 32 Bond restraints: 4557 Sorted by residual: bond pdb=" ND2 ASN A 5 " pdb="HD22 ASN A 5 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.82e+01 bond pdb=" NE1 TRP A 117 " pdb=" HE1 TRP A 117 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" NE2 GLN A 112 " pdb="HE21 GLN A 112 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.68e+01 bond pdb=" N LEU A 189 " pdb=" H LEU A 189 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.64e+01 bond pdb=" N PHE A 40 " pdb=" H PHE A 40 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.59e+01 ... (remaining 4552 not shown) Histogram of bond angle deviations from ideal: 100.50 - 107.19: 147 107.19 - 113.88: 5515 113.88 - 120.56: 1461 120.56 - 127.25: 1117 127.25 - 133.94: 35 Bond angle restraints: 8275 Sorted by residual: angle pdb=" CA LYS A 131 " pdb=" CB LYS A 131 " pdb=" CG LYS A 131 " ideal model delta sigma weight residual 114.10 117.59 -3.49 2.00e+00 2.50e-01 3.04e+00 angle pdb=" CA ARG A 173 " pdb=" CB ARG A 173 " pdb=" CG ARG A 173 " ideal model delta sigma weight residual 114.10 117.27 -3.17 2.00e+00 2.50e-01 2.52e+00 angle pdb=" CB LYS A 131 " pdb=" CG LYS A 131 " pdb=" CD LYS A 131 " ideal model delta sigma weight residual 111.30 107.72 3.58 2.30e+00 1.89e-01 2.42e+00 angle pdb=" N LYS A 131 " pdb=" CA LYS A 131 " pdb=" CB LYS A 131 " ideal model delta sigma weight residual 110.12 108.02 2.10 1.47e+00 4.63e-01 2.05e+00 angle pdb=" N ARG A 173 " pdb=" CA ARG A 173 " pdb=" CB ARG A 173 " ideal model delta sigma weight residual 110.28 108.24 2.04 1.55e+00 4.16e-01 1.73e+00 ... (remaining 8270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 1981 17.34 - 34.68: 106 34.68 - 52.02: 42 52.02 - 69.36: 9 69.36 - 86.71: 1 Dihedral angle restraints: 2139 sinusoidal: 1209 harmonic: 930 Sorted by residual: dihedral pdb=" CB MET A 66 " pdb=" CG MET A 66 " pdb=" SD MET A 66 " pdb=" CE MET A 66 " ideal model delta sinusoidal sigma weight residual -60.00 -115.14 55.14 3 1.50e+01 4.44e-03 9.33e+00 dihedral pdb=" CA ALA A 47 " pdb=" C ALA A 47 " pdb=" N THR A 48 " pdb=" CA THR A 48 " ideal model delta harmonic sigma weight residual 180.00 165.05 14.95 0 5.00e+00 4.00e-02 8.94e+00 dihedral pdb=" CA PHE A 32 " pdb=" C PHE A 32 " pdb=" N SER A 33 " pdb=" CA SER A 33 " ideal model delta harmonic sigma weight residual 180.00 165.57 14.43 0 5.00e+00 4.00e-02 8.32e+00 ... (remaining 2136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 237 0.029 - 0.059: 68 0.059 - 0.088: 34 0.088 - 0.118: 11 0.118 - 0.147: 1 Chirality restraints: 351 Sorted by residual: chirality pdb=" CA ILE A 124 " pdb=" N ILE A 124 " pdb=" C ILE A 124 " pdb=" CB ILE A 124 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA ILE A 153 " pdb=" N ILE A 153 " pdb=" C ILE A 153 " pdb=" CB ILE A 153 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.16e-01 chirality pdb=" CA ILE B 153 " pdb=" N ILE B 153 " pdb=" C ILE B 153 " pdb=" CB ILE B 153 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.84e-01 ... (remaining 348 not shown) Planarity restraints: 671 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 121 " -0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A 122 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 122 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 122 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 37 " 0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO A 38 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 48 " 0.015 5.00e-02 4.00e+02 2.26e-02 8.15e-01 pdb=" N PRO A 49 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 49 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 49 " 0.013 5.00e-02 4.00e+02 ... (remaining 668 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 357 2.21 - 2.81: 9071 2.81 - 3.40: 12721 3.40 - 4.00: 15898 4.00 - 4.60: 23935 Nonbonded interactions: 61982 Sorted by model distance: nonbonded pdb=" O HIS A 62 " pdb=" H MET A 66 " model vdw 1.612 1.850 nonbonded pdb=" H ILE A 150 " pdb=" OE2 GLU A 175 " model vdw 1.631 1.850 nonbonded pdb="HE21 GLN B 155 " pdb=" O GLU B 159 " model vdw 1.639 1.850 nonbonded pdb=" H SER B 149 " pdb=" OD2 ASP B 152 " model vdw 1.664 1.850 nonbonded pdb=" OD1 ASN A 195 " pdb=" H CYS A 198 " model vdw 1.665 1.850 ... (remaining 61977 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: 5 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.49 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will not be refined Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.030 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: 0.030 Extract box with map and model: 0.100 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 6.110 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:0.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:3.590 Internal consistency checks: 0.000 Total: 10.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 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 : 0.002 0.037 2296 Z= 0.160 Angle : 0.512 4.299 3115 Z= 0.272 Chirality : 0.037 0.147 351 Planarity : 0.004 0.034 406 Dihedral : 11.205 86.706 877 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.45), residues: 280 helix: -0.83 (0.34), residues: 187 sheet: -1.70 (1.32), residues: 9 loop : 0.53 (0.61), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 162 TYR 0.006 0.001 TYR B 169 PHE 0.002 0.001 PHE B 161 TRP 0.005 0.001 TRP A 117 HIS 0.001 0.001 HIS A 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.7361 (mp) cc_final: 0.6980 (mt) REVERT: B 192 GLN cc_start: 0.7960 (tp40) cc_final: 0.7435 (mm110) REVERT: B 199 LYS cc_start: 0.7659 (tttt) cc_final: 0.7435 (ttmt) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1853 time to fit residues: 17.2883 Evaluate side-chains 60 residues out of total 247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2296 Z= 0.277 Angle : 0.529 4.301 3115 Z= 0.268 Chirality : 0.039 0.134 351 Planarity : 0.004 0.032 406 Dihedral : 4.729 30.340 306 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.81 % Allowed : 7.69 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.46), residues: 280 helix: -0.12 (0.35), residues: 197 sheet: -1.19 (1.27), residues: 9 loop : 0.67 (0.63), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 162 TYR 0.005 0.001 TYR A 169 PHE 0.006 0.001 PHE A 32 TRP 0.006 0.001 TRP A 133 HIS 0.004 0.001 HIS A 120 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 ASN cc_start: 0.8024 (m-40) cc_final: 0.7803 (m-40) REVERT: B 192 GLN cc_start: 0.8024 (tp40) cc_final: 0.7445 (mm110) REVERT: B 199 LYS cc_start: 0.7751 (tttt) cc_final: 0.7535 (ttmt) outliers start: 2 outliers final: 0 residues processed: 67 average time/residue: 0.3677 time to fit residues: 27.8028 Evaluate side-chains 59 residues out of total 247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2296 Z= 0.199 Angle : 0.510 4.236 3115 Z= 0.252 Chirality : 0.037 0.133 351 Planarity : 0.003 0.032 406 Dihedral : 4.329 21.154 306 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.62 % Allowed : 10.53 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.46), residues: 280 helix: 0.36 (0.36), residues: 194 sheet: -1.63 (1.13), residues: 9 loop : 0.69 (0.61), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 132 TYR 0.004 0.001 TYR A 169 PHE 0.004 0.001 PHE A 32 TRP 0.005 0.001 TRP A 80 HIS 0.003 0.001 HIS A 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 ASN cc_start: 0.8009 (m-40) cc_final: 0.7798 (m-40) REVERT: B 175 GLU cc_start: 0.6515 (mt-10) cc_final: 0.6126 (mt-10) REVERT: B 192 GLN cc_start: 0.7983 (tp40) cc_final: 0.7402 (mm110) REVERT: B 193 ASN cc_start: 0.8888 (m110) cc_final: 0.8466 (m110) REVERT: B 199 LYS cc_start: 0.7781 (tttt) cc_final: 0.7548 (ttmt) REVERT: B 203 LYS cc_start: 0.6961 (mttt) cc_final: 0.6739 (mttp) outliers start: 4 outliers final: 0 residues processed: 63 average time/residue: 0.2940 time to fit residues: 20.7239 Evaluate side-chains 59 residues out of total 247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 4 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN B 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2296 Z= 0.187 Angle : 0.480 4.130 3115 Z= 0.238 Chirality : 0.036 0.133 351 Planarity : 0.004 0.041 406 Dihedral : 3.978 14.051 306 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.81 % Allowed : 11.74 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.48), residues: 280 helix: 0.83 (0.37), residues: 194 sheet: -2.03 (1.02), residues: 9 loop : 0.80 (0.63), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 132 TYR 0.005 0.001 TYR A 169 PHE 0.004 0.001 PHE A 32 TRP 0.005 0.001 TRP A 80 HIS 0.002 0.001 HIS A 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.6488 (mt-10) cc_final: 0.6084 (mt-10) REVERT: B 192 GLN cc_start: 0.7863 (tp40) cc_final: 0.7423 (mm110) REVERT: B 193 ASN cc_start: 0.8868 (m110) cc_final: 0.8483 (m110) REVERT: B 199 LYS cc_start: 0.7776 (tttt) cc_final: 0.7517 (ttmt) outliers start: 2 outliers final: 1 residues processed: 62 average time/residue: 0.2324 time to fit residues: 16.2260 Evaluate side-chains 59 residues out of total 247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 21 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN A 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2296 Z= 0.149 Angle : 0.470 4.060 3115 Z= 0.230 Chirality : 0.036 0.136 351 Planarity : 0.004 0.038 406 Dihedral : 3.651 12.055 306 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.81 % Allowed : 11.74 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.49), residues: 280 helix: 1.26 (0.38), residues: 194 sheet: -1.99 (0.95), residues: 9 loop : 0.89 (0.63), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 132 TYR 0.005 0.001 TYR A 169 PHE 0.003 0.001 PHE A 32 TRP 0.006 0.001 TRP A 80 HIS 0.002 0.000 HIS A 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 192 GLN cc_start: 0.7903 (tp40) cc_final: 0.7422 (mm110) REVERT: B 193 ASN cc_start: 0.8831 (m110) cc_final: 0.8429 (m110) REVERT: B 199 LYS cc_start: 0.7704 (tttt) cc_final: 0.7472 (ttmt) outliers start: 2 outliers final: 1 residues processed: 61 average time/residue: 0.1932 time to fit residues: 13.2520 Evaluate side-chains 57 residues out of total 247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2296 Z= 0.212 Angle : 0.489 4.134 3115 Z= 0.240 Chirality : 0.037 0.142 351 Planarity : 0.004 0.038 406 Dihedral : 3.745 12.520 306 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.40 % Allowed : 11.34 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.49), residues: 280 helix: 1.23 (0.38), residues: 194 sheet: -1.95 (1.02), residues: 9 loop : 0.95 (0.64), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 132 TYR 0.004 0.001 TYR B 169 PHE 0.005 0.001 PHE A 32 TRP 0.007 0.001 TRP A 184 HIS 0.002 0.001 HIS A 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 606.77 seconds wall clock time: 10 minutes 48.56 seconds (648.56 seconds total)