Starting phenix.real_space_refine (version: dev) on Sat Feb 18 01:44:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lq5_23481/02_2023/7lq5_23481_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lq5_23481/02_2023/7lq5_23481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lq5_23481/02_2023/7lq5_23481.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lq5_23481/02_2023/7lq5_23481.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lq5_23481/02_2023/7lq5_23481_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lq5_23481/02_2023/7lq5_23481_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.001 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 Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C ARG 139": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 6843 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1937 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 22, 'TRANS': 235} Chain: "B" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1937 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 22, 'TRANS': 235} Chain: "C" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1937 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 22, 'TRANS': 235} Chain: "A" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 344 Unusual residues: {'HEC': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 344 Unusual residues: {'HEC': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 344 Unusual residues: {'HEC': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 4.51, per 1000 atoms: 0.66 Number of scatterers: 6843 At special positions: 0 Unit cell: (75.348, 61.272, 205.344, 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) Fe 24 26.01 S 54 16.00 O 1215 8.00 N 1140 7.00 C 4410 6.00 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=72, symmetry=0 Number of additional bonds: simple=72, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 869.6 milliseconds 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1422 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 3 sheets defined 13.2% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 19 through 21 No H-bonds generated for 'chain 'A' and resid 19 through 21' Processing helix chain 'A' and resid 33 through 45 removed outlier: 4.919A pdb=" N GLN A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU A 43 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE A 44 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASN A 45 " --> pdb=" O HIS A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 190 through 193 No H-bonds generated for 'chain 'A' and resid 190 through 193' Processing helix chain 'A' and resid 211 through 214 No H-bonds generated for 'chain 'A' and resid 211 through 214' Processing helix chain 'A' and resid 245 through 251 Processing helix chain 'B' and resid 19 through 21 No H-bonds generated for 'chain 'B' and resid 19 through 21' Processing helix chain 'B' and resid 33 through 45 removed outlier: 4.919A pdb=" N GLN B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU B 43 " --> pdb=" O GLN B 39 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE B 44 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASN B 45 " --> pdb=" O HIS B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 156 No H-bonds generated for 'chain 'B' and resid 154 through 156' Processing helix chain 'B' and resid 190 through 193 No H-bonds generated for 'chain 'B' and resid 190 through 193' Processing helix chain 'B' and resid 211 through 214 No H-bonds generated for 'chain 'B' and resid 211 through 214' Processing helix chain 'B' and resid 245 through 251 Processing helix chain 'C' and resid 19 through 21 No H-bonds generated for 'chain 'C' and resid 19 through 21' Processing helix chain 'C' and resid 33 through 45 removed outlier: 4.919A pdb=" N GLN C 38 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU C 43 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE C 44 " --> pdb=" O HIS C 40 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASN C 45 " --> pdb=" O HIS C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 156 No H-bonds generated for 'chain 'C' and resid 154 through 156' Processing helix chain 'C' and resid 190 through 193 No H-bonds generated for 'chain 'C' and resid 190 through 193' Processing helix chain 'C' and resid 211 through 214 No H-bonds generated for 'chain 'C' and resid 211 through 214' Processing helix chain 'C' and resid 245 through 251 Processing sheet with id= A, first strand: chain 'A' and resid 139 through 142 Processing sheet with id= B, first strand: chain 'B' and resid 139 through 142 Processing sheet with id= C, first strand: chain 'C' and resid 139 through 142 36 hydrogen bonds defined for protein. 99 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: 1.46 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 2867 1.38 - 1.56: 4150 1.56 - 1.73: 15 1.73 - 1.90: 60 1.90 - 2.08: 96 Bond restraints: 7188 Sorted by residual: bond pdb=" N VAL C 230 " pdb=" CA VAL C 230 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.30e+00 bond pdb=" N VAL A 230 " pdb=" CA VAL A 230 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.96e+00 bond pdb=" N VAL B 230 " pdb=" CA VAL B 230 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.73e+00 bond pdb=" N SER B 177 " pdb=" CA SER B 177 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.27e-02 6.20e+03 7.56e+00 bond pdb=" N SER A 177 " pdb=" CA SER A 177 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.27e-02 6.20e+03 7.50e+00 ... (remaining 7183 not shown) Histogram of bond angle deviations from ideal: 85.54 - 104.27: 276 104.27 - 122.99: 8307 122.99 - 141.72: 1560 141.72 - 160.44: 0 160.44 - 179.17: 48 Bond angle restraints: 10191 Sorted by residual: angle pdb=" N ASP C 220 " pdb=" CA ASP C 220 " pdb=" C ASP C 220 " ideal model delta sigma weight residual 110.53 116.76 -6.23 1.32e+00 5.74e-01 2.23e+01 angle pdb=" N ASP A 220 " pdb=" CA ASP A 220 " pdb=" C ASP A 220 " ideal model delta sigma weight residual 110.53 116.74 -6.21 1.32e+00 5.74e-01 2.21e+01 angle pdb=" N ASP B 220 " pdb=" CA ASP B 220 " pdb=" C ASP B 220 " ideal model delta sigma weight residual 110.53 116.73 -6.20 1.32e+00 5.74e-01 2.21e+01 angle pdb=" N SER B 221 " pdb=" CA SER B 221 " pdb=" C SER B 221 " ideal model delta sigma weight residual 110.07 115.15 -5.08 1.26e+00 6.30e-01 1.63e+01 angle pdb=" N SER A 221 " pdb=" CA SER A 221 " pdb=" C SER A 221 " ideal model delta sigma weight residual 110.07 115.14 -5.07 1.26e+00 6.30e-01 1.62e+01 ... (remaining 10186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 3054 16.68 - 33.36: 435 33.36 - 50.04: 135 50.04 - 66.72: 30 66.72 - 83.40: 36 Dihedral angle restraints: 3690 sinusoidal: 1485 harmonic: 2205 Sorted by residual: dihedral pdb=" CA HIS C 30 " pdb=" C HIS C 30 " pdb=" N VAL C 31 " pdb=" CA VAL C 31 " ideal model delta harmonic sigma weight residual -180.00 -150.54 -29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA HIS A 30 " pdb=" C HIS A 30 " pdb=" N VAL A 31 " pdb=" CA VAL A 31 " ideal model delta harmonic sigma weight residual -180.00 -150.55 -29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA HIS B 30 " pdb=" C HIS B 30 " pdb=" N VAL B 31 " pdb=" CA VAL B 31 " ideal model delta harmonic sigma weight residual -180.00 -150.58 -29.42 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 3687 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 512 0.054 - 0.107: 288 0.107 - 0.161: 106 0.161 - 0.214: 6 0.214 - 0.267: 3 Chirality restraints: 915 Sorted by residual: chirality pdb=" CB THR B 94 " pdb=" CA THR B 94 " pdb=" OG1 THR B 94 " pdb=" CG2 THR B 94 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB THR C 94 " pdb=" CA THR C 94 " pdb=" OG1 THR C 94 " pdb=" CG2 THR C 94 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB THR A 94 " pdb=" CA THR A 94 " pdb=" OG1 THR A 94 " pdb=" CG2 THR A 94 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 912 not shown) Planarity restraints: 1251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND HEC B 303 " 0.004 2.00e-02 2.50e+03 1.43e-02 4.58e+00 pdb=" C1D HEC B 303 " -0.001 2.00e-02 2.50e+03 pdb=" C2D HEC B 303 " 0.032 2.00e-02 2.50e+03 pdb=" C3D HEC B 303 " -0.016 2.00e-02 2.50e+03 pdb=" C4D HEC B 303 " -0.006 2.00e-02 2.50e+03 pdb=" CAD HEC B 303 " 0.012 2.00e-02 2.50e+03 pdb=" CHA HEC B 303 " -0.005 2.00e-02 2.50e+03 pdb=" CHD HEC B 303 " -0.000 2.00e-02 2.50e+03 pdb=" CMD HEC B 303 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND HEC C 303 " 0.004 2.00e-02 2.50e+03 1.42e-02 4.56e+00 pdb=" C1D HEC C 303 " -0.001 2.00e-02 2.50e+03 pdb=" C2D HEC C 303 " 0.031 2.00e-02 2.50e+03 pdb=" C3D HEC C 303 " -0.015 2.00e-02 2.50e+03 pdb=" C4D HEC C 303 " -0.007 2.00e-02 2.50e+03 pdb=" CAD HEC C 303 " 0.012 2.00e-02 2.50e+03 pdb=" CHA HEC C 303 " -0.005 2.00e-02 2.50e+03 pdb=" CHD HEC C 303 " 0.000 2.00e-02 2.50e+03 pdb=" CMD HEC C 303 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 166 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C ASP B 166 " -0.037 2.00e-02 2.50e+03 pdb=" O ASP B 166 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO B 167 " 0.012 2.00e-02 2.50e+03 ... (remaining 1248 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 66 2.47 - 3.07: 4999 3.07 - 3.68: 10894 3.68 - 4.29: 16062 4.29 - 4.90: 25628 Nonbonded interactions: 57649 Sorted by model distance: nonbonded pdb=" NE2 HIS C 194 " pdb="FE HEC C 306 " model vdw 1.857 3.080 nonbonded pdb=" NE2 HIS B 194 " pdb="FE HEC B 306 " model vdw 1.858 3.080 nonbonded pdb=" NE2 HIS A 194 " pdb="FE HEC A 306 " model vdw 1.858 3.080 nonbonded pdb=" NE2 HIS A 158 " pdb="FE HEC A 305 " model vdw 2.009 3.080 nonbonded pdb=" NE2 HIS C 158 " pdb="FE HEC C 305 " model vdw 2.009 3.080 ... (remaining 57644 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 24 7.16 5 S 54 5.16 5 C 4410 2.51 5 N 1140 2.21 5 O 1215 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 4.010 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: 12.430 Check model and map are aligned: 0.090 Process input model: 22.340 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.070 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 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 : 0.013 0.119 7188 Z= 0.816 Angle : 1.307 7.053 10191 Z= 0.644 Chirality : 0.068 0.267 915 Planarity : 0.009 0.044 1251 Dihedral : 19.666 83.396 2268 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 27.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.89 % Favored : 87.11 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.95 (0.24), residues: 768 helix: -4.81 (0.13), residues: 126 sheet: None (None), residues: 0 loop : -3.31 (0.21), residues: 642 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 0.901 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 109 average time/residue: 0.1992 time to fit residues: 28.8353 Evaluate side-chains 69 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.819 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1063 time to fit residues: 1.4161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN B 158 HIS B 199 ASN B 249 GLN C 158 HIS C 199 ASN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 7188 Z= 0.294 Angle : 0.899 13.339 10191 Z= 0.344 Chirality : 0.051 0.213 915 Planarity : 0.006 0.048 1251 Dihedral : 18.166 88.705 987 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer Outliers : 6.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.27), residues: 768 helix: -3.89 (0.27), residues: 108 sheet: None (None), residues: 0 loop : -2.40 (0.23), residues: 660 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 81 time to evaluate : 0.741 Fit side-chains outliers start: 42 outliers final: 25 residues processed: 117 average time/residue: 0.1782 time to fit residues: 28.5146 Evaluate side-chains 93 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 68 time to evaluate : 0.810 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.0689 time to fit residues: 4.0717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 0.0980 chunk 73 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 7188 Z= 0.315 Angle : 0.956 14.097 10191 Z= 0.339 Chirality : 0.050 0.161 915 Planarity : 0.006 0.045 1251 Dihedral : 18.232 89.101 987 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer Outliers : 3.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.28), residues: 768 helix: -3.41 (0.36), residues: 108 sheet: None (None), residues: 0 loop : -2.14 (0.24), residues: 660 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 80 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 16 residues processed: 100 average time/residue: 0.1704 time to fit residues: 24.0088 Evaluate side-chains 92 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 0.735 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 2 residues processed: 16 average time/residue: 0.0744 time to fit residues: 3.0125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 68 optimal weight: 0.3980 chunk 72 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.070 7188 Z= 0.328 Angle : 0.961 14.052 10191 Z= 0.344 Chirality : 0.050 0.140 915 Planarity : 0.006 0.043 1251 Dihedral : 18.076 89.317 987 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.02 % Favored : 86.98 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.29), residues: 768 helix: -3.28 (0.38), residues: 108 sheet: None (None), residues: 0 loop : -2.06 (0.24), residues: 660 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 110 average time/residue: 0.2016 time to fit residues: 30.3173 Evaluate side-chains 91 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.751 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 13 average time/residue: 0.0642 time to fit residues: 2.4028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 37 optimal weight: 0.0980 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 158 HIS A 249 GLN C 86 ASN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 7188 Z= 0.264 Angle : 0.883 12.584 10191 Z= 0.329 Chirality : 0.049 0.139 915 Planarity : 0.006 0.045 1251 Dihedral : 17.656 89.611 987 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.37 % Favored : 87.63 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.29), residues: 768 helix: -3.14 (0.40), residues: 108 sheet: None (None), residues: 0 loop : -1.94 (0.24), residues: 660 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 87 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 102 average time/residue: 0.1646 time to fit residues: 23.7146 Evaluate side-chains 91 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.727 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 13 average time/residue: 0.0835 time to fit residues: 2.8198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 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 249 GLN B 86 ASN ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 7188 Z= 0.294 Angle : 0.926 12.502 10191 Z= 0.338 Chirality : 0.050 0.227 915 Planarity : 0.006 0.046 1251 Dihedral : 17.401 89.608 987 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.89 % Favored : 87.11 % Rotamer Outliers : 3.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.29), residues: 768 helix: -3.10 (0.40), residues: 108 sheet: None (None), residues: 0 loop : -1.92 (0.24), residues: 660 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 87 time to evaluate : 0.742 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: symmetry clash outliers start: 24 outliers final: 18 residues processed: 107 average time/residue: 0.1710 time to fit residues: 25.6435 Evaluate side-chains 87 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 69 time to evaluate : 0.792 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 18 average time/residue: 0.0737 time to fit residues: 3.3096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.0770 chunk 41 optimal weight: 0.0670 chunk 52 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 28 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 HIS ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 7188 Z= 0.248 Angle : 0.888 11.618 10191 Z= 0.337 Chirality : 0.049 0.214 915 Planarity : 0.006 0.047 1251 Dihedral : 17.020 89.434 987 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.37 % Favored : 87.63 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.29), residues: 768 helix: -2.67 (0.45), residues: 90 sheet: None (None), residues: 0 loop : -1.86 (0.24), residues: 678 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 97 average time/residue: 0.1475 time to fit residues: 20.4621 Evaluate side-chains 80 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 0.640 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 11 average time/residue: 0.0629 time to fit residues: 2.0694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 63 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN C 117 ASN C 191 ASN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 7188 Z= 0.332 Angle : 0.990 12.457 10191 Z= 0.363 Chirality : 0.051 0.190 915 Planarity : 0.006 0.047 1251 Dihedral : 17.204 89.501 987 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.02 % Favored : 86.98 % Rotamer Outliers : 2.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.29), residues: 768 helix: -3.09 (0.39), residues: 108 sheet: None (None), residues: 0 loop : -1.81 (0.24), residues: 660 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 15 residues processed: 82 average time/residue: 0.1711 time to fit residues: 20.0841 Evaluate side-chains 80 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 0.738 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 15 average time/residue: 0.0717 time to fit residues: 2.8779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 44 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 89 ASN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 7188 Z= 0.313 Angle : 0.961 12.147 10191 Z= 0.358 Chirality : 0.051 0.178 915 Planarity : 0.006 0.048 1251 Dihedral : 17.211 89.853 987 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.41 % Favored : 86.59 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.29), residues: 768 helix: -3.07 (0.40), residues: 108 sheet: None (None), residues: 0 loop : -1.79 (0.24), residues: 660 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 81 average time/residue: 0.1668 time to fit residues: 19.1146 Evaluate side-chains 75 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.801 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 9 average time/residue: 0.0689 time to fit residues: 2.0651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 7188 Z= 0.303 Angle : 0.955 11.652 10191 Z= 0.356 Chirality : 0.051 0.169 915 Planarity : 0.006 0.066 1251 Dihedral : 17.341 89.407 987 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.41 % Favored : 86.59 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.29), residues: 768 helix: -2.78 (0.44), residues: 90 sheet: None (None), residues: 0 loop : -1.83 (0.24), residues: 678 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 13 residues processed: 76 average time/residue: 0.1805 time to fit residues: 19.2088 Evaluate side-chains 77 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.719 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 13 average time/residue: 0.0786 time to fit residues: 2.7333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 ASN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.124810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.099345 restraints weight = 9982.168| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.67 r_work: 0.3305 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 7188 Z= 0.310 Angle : 0.965 12.084 10191 Z= 0.359 Chirality : 0.051 0.168 915 Planarity : 0.006 0.062 1251 Dihedral : 17.336 89.763 987 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.93 % Favored : 86.07 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.29), residues: 768 helix: -3.00 (0.40), residues: 108 sheet: None (None), residues: 0 loop : -1.74 (0.24), residues: 660 =============================================================================== Job complete usr+sys time: 1716.77 seconds wall clock time: 32 minutes 18.59 seconds (1938.59 seconds total)