Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 02:26:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk0_25168/04_2023/7sk0_25168_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk0_25168/04_2023/7sk0_25168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk0_25168/04_2023/7sk0_25168.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk0_25168/04_2023/7sk0_25168.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk0_25168/04_2023/7sk0_25168_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk0_25168/04_2023/7sk0_25168_updated.pdb" } resolution = 3.33 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= 0.264 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 5 8.98 5 S 16 5.16 5 C 2781 2.51 5 N 654 2.21 5 O 712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 65": "OE1" <-> "OE2" Residue "A ARG 163": "NH1" <-> "NH2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B ARG 163": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 4168 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2074 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain: "B" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2073 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 13 Unusual residues: {' K': 5, 'OCT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'OCT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.85, per 1000 atoms: 0.68 Number of scatterers: 4168 At special positions: 0 Unit cell: (69.357, 69.357, 90.96, 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) K 5 19.00 S 16 16.00 O 712 8.00 N 654 7.00 C 2781 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS B 69 " distance=2.04 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: 2.24 Conformation dependent library (CDL) restraints added in 687.8 milliseconds 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 952 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 0 sheets defined 76.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 25 through 66 removed outlier: 4.087A pdb=" N LEU A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Proline residue: A 47 - end of helix Processing helix chain 'A' and resid 72 through 88 Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 128 through 160 removed outlier: 3.528A pdb=" N ILE A 140 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Proline residue: A 143 - end of helix removed outlier: 3.592A pdb=" N VAL A 158 " --> pdb=" O GLN A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 172 Processing helix chain 'A' and resid 176 through 195 removed outlier: 3.543A pdb=" N ALA A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 181 " --> pdb=" O GLN A 177 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 206 Processing helix chain 'A' and resid 212 through 224 Processing helix chain 'A' and resid 242 through 269 Processing helix chain 'A' and resid 271 through 279 Processing helix chain 'B' and resid 25 through 66 removed outlier: 4.087A pdb=" N LEU B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) Proline residue: B 47 - end of helix Processing helix chain 'B' and resid 72 through 88 Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 128 through 160 removed outlier: 3.529A pdb=" N ILE B 140 " --> pdb=" O ILE B 136 " (cutoff:3.500A) Proline residue: B 143 - end of helix removed outlier: 3.592A pdb=" N VAL B 158 " --> pdb=" O GLN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 172 Processing helix chain 'B' and resid 176 through 195 removed outlier: 3.542A pdb=" N ALA B 180 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE B 181 " --> pdb=" O GLN B 177 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL B 185 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 206 Processing helix chain 'B' and resid 212 through 224 Processing helix chain 'B' and resid 242 through 269 Processing helix chain 'B' and resid 271 through 279 282 hydrogen bonds defined for protein. 846 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: 1.09 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1250 1.34 - 1.46: 1152 1.46 - 1.58: 1854 1.58 - 1.70: 0 1.70 - 1.82: 20 Bond restraints: 4276 Sorted by residual: bond pdb=" CG LEU B 79 " pdb=" CD1 LEU B 79 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.34e+00 bond pdb=" CG LEU A 79 " pdb=" CD1 LEU A 79 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.30e+00 bond pdb=" CG1 ILE A 258 " pdb=" CD1 ILE A 258 " ideal model delta sigma weight residual 1.513 1.433 0.080 3.90e-02 6.57e+02 4.25e+00 bond pdb=" CG1 ILE B 258 " pdb=" CD1 ILE B 258 " ideal model delta sigma weight residual 1.513 1.434 0.079 3.90e-02 6.57e+02 4.14e+00 bond pdb=" CB GLU A 207 " pdb=" CG GLU A 207 " ideal model delta sigma weight residual 1.520 1.463 0.057 3.00e-02 1.11e+03 3.64e+00 ... (remaining 4271 not shown) Histogram of bond angle deviations from ideal: 98.08 - 105.28: 52 105.28 - 112.48: 2062 112.48 - 119.67: 1549 119.67 - 126.87: 2080 126.87 - 134.06: 56 Bond angle restraints: 5799 Sorted by residual: angle pdb=" N ASP B 103 " pdb=" CA ASP B 103 " pdb=" C ASP B 103 " ideal model delta sigma weight residual 109.24 103.89 5.35 1.51e+00 4.39e-01 1.26e+01 angle pdb=" N ASP A 103 " pdb=" CA ASP A 103 " pdb=" C ASP A 103 " ideal model delta sigma weight residual 109.24 103.91 5.33 1.51e+00 4.39e-01 1.25e+01 angle pdb=" C ASN A 95 " pdb=" N ALA A 96 " pdb=" CA ALA A 96 " ideal model delta sigma weight residual 121.54 128.01 -6.47 1.91e+00 2.74e-01 1.15e+01 angle pdb=" C ASN B 95 " pdb=" N ALA B 96 " pdb=" CA ALA B 96 " ideal model delta sigma weight residual 121.54 127.98 -6.44 1.91e+00 2.74e-01 1.14e+01 angle pdb=" C TRP A 100 " pdb=" N ASN A 101 " pdb=" CA ASN A 101 " ideal model delta sigma weight residual 120.38 124.45 -4.07 1.37e+00 5.33e-01 8.84e+00 ... (remaining 5794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 2155 15.79 - 31.57: 222 31.57 - 47.36: 40 47.36 - 63.15: 14 63.15 - 78.94: 8 Dihedral angle restraints: 2439 sinusoidal: 951 harmonic: 1488 Sorted by residual: dihedral pdb=" N ASN B 87 " pdb=" CA ASN B 87 " pdb=" CB ASN B 87 " pdb=" CG ASN B 87 " ideal model delta sinusoidal sigma weight residual -60.00 -113.65 53.65 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" N ASN A 87 " pdb=" CA ASN A 87 " pdb=" CB ASN A 87 " pdb=" CG ASN A 87 " ideal model delta sinusoidal sigma weight residual -60.00 -113.62 53.62 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" CB MET A 279 " pdb=" CG MET A 279 " pdb=" SD MET A 279 " pdb=" CE MET A 279 " ideal model delta sinusoidal sigma weight residual -180.00 -127.29 -52.71 3 1.50e+01 4.44e-03 9.14e+00 ... (remaining 2436 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 378 0.039 - 0.078: 160 0.078 - 0.117: 86 0.117 - 0.156: 22 0.156 - 0.194: 12 Chirality restraints: 658 Sorted by residual: chirality pdb=" CB VAL A 92 " pdb=" CA VAL A 92 " pdb=" CG1 VAL A 92 " pdb=" CG2 VAL A 92 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.45e-01 chirality pdb=" CG LEU A 254 " pdb=" CB LEU A 254 " pdb=" CD1 LEU A 254 " pdb=" CD2 LEU A 254 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CG LEU B 254 " pdb=" CB LEU B 254 " pdb=" CD1 LEU B 254 " pdb=" CD2 LEU B 254 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.24e-01 ... (remaining 655 not shown) Planarity restraints: 712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 254 " 0.022 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C LEU A 254 " -0.077 2.00e-02 2.50e+03 pdb=" O LEU A 254 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU A 255 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 254 " -0.022 2.00e-02 2.50e+03 4.41e-02 1.95e+01 pdb=" C LEU B 254 " 0.076 2.00e-02 2.50e+03 pdb=" O LEU B 254 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU B 255 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 80 " 0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C GLY A 80 " -0.057 2.00e-02 2.50e+03 pdb=" O GLY A 80 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG A 81 " 0.019 2.00e-02 2.50e+03 ... (remaining 709 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.63: 46 2.63 - 3.26: 4809 3.26 - 3.89: 8445 3.89 - 4.51: 11240 4.51 - 5.14: 16866 Nonbonded interactions: 41406 Sorted by model distance: nonbonded pdb=" OG SER B 71 " pdb=" OE1 GLN B 74 " model vdw 2.005 2.440 nonbonded pdb=" OG SER A 71 " pdb=" OE1 GLN A 74 " model vdw 2.005 2.440 nonbonded pdb=" ND2 ASN A 87 " pdb=" O GLY B 229 " model vdw 2.141 2.520 nonbonded pdb=" O GLY A 229 " pdb=" ND2 ASN B 87 " model vdw 2.230 2.520 nonbonded pdb=" O SER B 116 " pdb=" OG1 THR B 117 " model vdw 2.270 2.440 ... (remaining 41401 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' and (resid 24 through 279 or (resid 280 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2)) or resid 401)) selection = chain 'B' } 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: 0.390 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: 1.970 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.310 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.080 4276 Z= 0.558 Angle : 1.042 8.092 5799 Z= 0.587 Chirality : 0.058 0.194 658 Planarity : 0.008 0.044 712 Dihedral : 14.222 78.936 1484 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 0.44 % 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: 0.35 (0.36), residues: 510 helix: 0.73 (0.24), residues: 396 sheet: None (None), residues: 0 loop : -1.30 (0.65), residues: 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 0.500 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 101 average time/residue: 0.1196 time to fit residues: 16.3497 Evaluate side-chains 86 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.437 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 0.0170 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN B 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 4276 Z= 0.227 Angle : 0.647 5.676 5799 Z= 0.349 Chirality : 0.043 0.181 658 Planarity : 0.005 0.027 712 Dihedral : 4.755 15.207 568 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 2.65 % 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: 2.01 (0.39), residues: 510 helix: 1.97 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -0.77 (0.69), residues: 120 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 106 average time/residue: 0.1102 time to fit residues: 15.8917 Evaluate side-chains 101 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.451 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0559 time to fit residues: 1.4683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN B 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 4276 Z= 0.255 Angle : 0.629 7.083 5799 Z= 0.331 Chirality : 0.043 0.220 658 Planarity : 0.005 0.041 712 Dihedral : 4.796 16.757 568 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.40), residues: 510 helix: 2.00 (0.26), residues: 400 sheet: None (None), residues: 0 loop : -0.53 (0.76), residues: 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.489 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 98 average time/residue: 0.1056 time to fit residues: 14.4453 Evaluate side-chains 94 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.482 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0522 time to fit residues: 0.8515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN B 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 4276 Z= 0.270 Angle : 0.596 5.811 5799 Z= 0.326 Chirality : 0.042 0.166 658 Planarity : 0.004 0.035 712 Dihedral : 4.766 19.090 568 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.39), residues: 510 helix: 2.01 (0.26), residues: 400 sheet: None (None), residues: 0 loop : -0.80 (0.75), residues: 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 100 average time/residue: 0.1054 time to fit residues: 14.8795 Evaluate side-chains 96 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.490 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0463 time to fit residues: 1.0078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 41 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 4276 Z= 0.253 Angle : 0.590 5.899 5799 Z= 0.318 Chirality : 0.041 0.176 658 Planarity : 0.004 0.033 712 Dihedral : 4.723 20.509 568 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 0.66 % 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: 2.02 (0.39), residues: 510 helix: 2.00 (0.25), residues: 398 sheet: None (None), residues: 0 loop : -1.08 (0.73), residues: 112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 95 average time/residue: 0.1065 time to fit residues: 14.3492 Evaluate side-chains 90 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0634 time to fit residues: 0.9088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 0.0470 chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 46 optimal weight: 0.2980 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 4276 Z= 0.207 Angle : 0.559 5.880 5799 Z= 0.303 Chirality : 0.040 0.149 658 Planarity : 0.004 0.037 712 Dihedral : 4.557 20.205 568 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 0.44 % 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: 2.10 (0.39), residues: 510 helix: 2.08 (0.26), residues: 398 sheet: None (None), residues: 0 loop : -1.18 (0.71), residues: 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 97 average time/residue: 0.1089 time to fit residues: 15.0778 Evaluate side-chains 93 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.518 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0510 time to fit residues: 0.7564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.0570 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 4276 Z= 0.224 Angle : 0.590 9.666 5799 Z= 0.314 Chirality : 0.041 0.189 658 Planarity : 0.004 0.037 712 Dihedral : 4.517 20.818 568 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 0.66 % 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: 2.11 (0.39), residues: 510 helix: 2.04 (0.25), residues: 400 sheet: None (None), residues: 0 loop : -1.06 (0.72), residues: 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 0.481 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 96 average time/residue: 0.1022 time to fit residues: 13.8626 Evaluate side-chains 94 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.488 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0478 time to fit residues: 0.8501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 46 optimal weight: 0.0070 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 4276 Z= 0.222 Angle : 0.585 6.051 5799 Z= 0.316 Chirality : 0.042 0.226 658 Planarity : 0.004 0.037 712 Dihedral : 4.483 20.548 568 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 0.44 % 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: 2.12 (0.39), residues: 510 helix: 2.12 (0.26), residues: 398 sheet: None (None), residues: 0 loop : -1.27 (0.71), residues: 112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 96 average time/residue: 0.1042 time to fit residues: 14.1764 Evaluate side-chains 95 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.502 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0404 time to fit residues: 0.6825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.0270 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 4276 Z= 0.236 Angle : 0.642 11.909 5799 Z= 0.334 Chirality : 0.042 0.220 658 Planarity : 0.004 0.038 712 Dihedral : 4.487 20.857 568 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 0.22 % 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: 2.08 (0.39), residues: 510 helix: 2.11 (0.26), residues: 398 sheet: None (None), residues: 0 loop : -1.39 (0.69), residues: 112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.471 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.1025 time to fit residues: 14.1441 Evaluate side-chains 96 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.450 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 4276 Z= 0.281 Angle : 0.684 12.115 5799 Z= 0.354 Chirality : 0.044 0.247 658 Planarity : 0.004 0.039 712 Dihedral : 4.611 21.733 568 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.39), residues: 510 helix: 1.89 (0.25), residues: 400 sheet: None (None), residues: 0 loop : -1.27 (0.70), residues: 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 101 average time/residue: 0.1163 time to fit residues: 16.2326 Evaluate side-chains 96 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.469 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0493 time to fit residues: 0.7846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 1 optimal weight: 0.0040 chunk 31 optimal weight: 0.1980 chunk 30 optimal weight: 0.5980 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.225027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.176332 restraints weight = 5224.250| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 2.66 r_work: 0.3966 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 4276 Z= 0.230 Angle : 0.685 12.972 5799 Z= 0.347 Chirality : 0.042 0.230 658 Planarity : 0.004 0.039 712 Dihedral : 4.558 21.033 568 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 0.00 % 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: 2.04 (0.39), residues: 510 helix: 2.05 (0.26), residues: 400 sheet: None (None), residues: 0 loop : -1.32 (0.70), residues: 110 =============================================================================== Job complete usr+sys time: 1207.50 seconds wall clock time: 22 minutes 23.07 seconds (1343.07 seconds total)