Starting phenix.real_space_refine on Tue Feb 13 07:42:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk0_25168/02_2024/7sk0_25168_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk0_25168/02_2024/7sk0_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_25168/02_2024/7sk0_25168.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk0_25168/02_2024/7sk0_25168.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk0_25168/02_2024/7sk0_25168_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk0_25168/02_2024/7sk0_25168_updated.pdb" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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-dev-5238/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: 2.78, per 1000 atoms: 0.67 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: 1.93 Conformation dependent library (CDL) restraints added in 734.6 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: 0.71 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: 1.02 Time building geometry restraints manager: 2.09 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: 0.400 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: 1.850 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.310 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.700 ------------------------------------------------------------------------------- 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 % Allowed : 1.33 % Favored : 98.23 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 100 HIS 0.013 0.003 HIS A 122 PHE 0.039 0.004 PHE B 144 TYR 0.031 0.005 TYR A 237 ARG 0.013 0.002 ARG B 163 *********************** 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 : 0.442 Fit side-chains revert: symmetry clash REVERT: A 74 GLN cc_start: 0.7034 (mp10) cc_final: 0.6579 (mp10) REVERT: B 28 LEU cc_start: 0.8157 (mt) cc_final: 0.7842 (mt) REVERT: B 74 GLN cc_start: 0.7280 (mp10) cc_final: 0.6809 (mp10) REVERT: B 87 ASN cc_start: 0.7164 (OUTLIER) cc_final: 0.6932 (t0) REVERT: B 243 GLU cc_start: 0.7398 (mp0) cc_final: 0.7169 (mp0) outliers start: 2 outliers final: 0 residues processed: 101 average time/residue: 0.1139 time to fit residues: 15.6559 Evaluate side-chains 87 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 ASN 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: 0.7980 chunk 20 optimal weight: 0.3980 chunk 39 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN B 77 GLN B 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4276 Z= 0.243 Angle : 0.643 5.680 5799 Z= 0.348 Chirality : 0.043 0.182 658 Planarity : 0.005 0.027 712 Dihedral : 5.419 53.003 570 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.88 % Allowed : 6.86 % Favored : 90.27 % 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: 1.98 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -0.81 (0.69), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 210 HIS 0.002 0.001 HIS B 122 PHE 0.016 0.002 PHE B 133 TYR 0.013 0.002 TYR A 88 ARG 0.002 0.001 ARG B 81 *********************** 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 115 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLN cc_start: 0.7000 (mp10) cc_final: 0.6379 (mp10) REVERT: A 243 GLU cc_start: 0.7321 (mp0) cc_final: 0.6987 (mp0) REVERT: A 260 MET cc_start: 0.7539 (mmm) cc_final: 0.7315 (mmt) REVERT: A 279 MET cc_start: 0.3648 (ttt) cc_final: 0.3308 (ttp) REVERT: B 28 LEU cc_start: 0.7803 (mt) cc_final: 0.7502 (mt) REVERT: B 74 GLN cc_start: 0.7182 (mp10) cc_final: 0.6545 (mp10) REVERT: B 243 GLU cc_start: 0.7433 (mp0) cc_final: 0.7120 (mp0) REVERT: B 276 PHE cc_start: 0.7305 (t80) cc_final: 0.6955 (t80) outliers start: 13 outliers final: 9 residues processed: 103 average time/residue: 0.1162 time to fit residues: 16.2021 Evaluate side-chains 102 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN B 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.2800 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 : 0.605 7.674 5799 Z= 0.322 Chirality : 0.043 0.217 658 Planarity : 0.005 0.042 712 Dihedral : 4.727 16.861 568 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.65 % Allowed : 9.29 % Favored : 88.05 % 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: 2.25 (0.40), residues: 510 helix: 2.05 (0.26), residues: 400 sheet: None (None), residues: 0 loop : -0.59 (0.76), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 100 HIS 0.003 0.001 HIS B 122 PHE 0.016 0.002 PHE A 144 TYR 0.012 0.002 TYR A 88 ARG 0.003 0.001 ARG A 53 *********************** 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 111 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLN cc_start: 0.7155 (mp10) cc_final: 0.6378 (mp10) REVERT: A 243 GLU cc_start: 0.7398 (mp0) cc_final: 0.7046 (mp0) REVERT: B 28 LEU cc_start: 0.7762 (mt) cc_final: 0.7450 (mt) REVERT: B 49 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6777 (tm-30) REVERT: B 74 GLN cc_start: 0.7213 (mp10) cc_final: 0.6668 (mp10) REVERT: B 243 GLU cc_start: 0.7503 (mp0) cc_final: 0.7149 (mp0) outliers start: 12 outliers final: 9 residues processed: 100 average time/residue: 0.1066 time to fit residues: 14.8532 Evaluate side-chains 103 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.0870 chunk 48 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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: 0.6582 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4276 Z= 0.232 Angle : 0.567 8.256 5799 Z= 0.306 Chirality : 0.041 0.181 658 Planarity : 0.004 0.040 712 Dihedral : 4.647 17.900 568 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.10 % Allowed : 10.40 % Favored : 86.50 % 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: 2.38 (0.40), residues: 510 helix: 2.19 (0.26), residues: 400 sheet: None (None), residues: 0 loop : -0.74 (0.76), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 102 HIS 0.002 0.001 HIS B 122 PHE 0.014 0.002 PHE B 133 TYR 0.010 0.001 TYR A 88 ARG 0.002 0.000 ARG A 62 *********************** 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 109 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7529 (tt) REVERT: A 74 GLN cc_start: 0.7159 (mp10) cc_final: 0.6410 (mp10) REVERT: B 49 GLU cc_start: 0.7162 (tm-30) cc_final: 0.6945 (tm-30) REVERT: B 56 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7400 (tt) REVERT: B 74 GLN cc_start: 0.7153 (mp10) cc_final: 0.6350 (mp10) REVERT: B 260 MET cc_start: 0.7756 (mmm) cc_final: 0.7536 (mmm) REVERT: B 279 MET cc_start: 0.4671 (ttt) cc_final: 0.4458 (ttp) outliers start: 14 outliers final: 8 residues processed: 99 average time/residue: 0.0863 time to fit residues: 12.1737 Evaluate side-chains 102 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 TYR 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: 0.9990 chunk 19 optimal weight: 0.5980 chunk 41 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 24 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4276 Z= 0.246 Angle : 0.567 5.803 5799 Z= 0.307 Chirality : 0.041 0.204 658 Planarity : 0.004 0.040 712 Dihedral : 4.630 19.522 568 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.21 % Allowed : 12.39 % Favored : 85.40 % 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: 2.26 (0.39), residues: 510 helix: 2.14 (0.26), residues: 400 sheet: None (None), residues: 0 loop : -0.92 (0.74), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 102 HIS 0.002 0.000 HIS B 122 PHE 0.012 0.002 PHE B 133 TYR 0.009 0.001 TYR A 88 ARG 0.002 0.000 ARG A 62 *********************** 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 109 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7511 (tp) REVERT: A 74 GLN cc_start: 0.7141 (mp10) cc_final: 0.6345 (mp10) REVERT: A 279 MET cc_start: 0.4302 (ttt) cc_final: 0.3455 (ttm) REVERT: B 31 LEU cc_start: 0.8480 (tp) cc_final: 0.8202 (mm) REVERT: B 56 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7169 (tt) REVERT: B 74 GLN cc_start: 0.7132 (mp10) cc_final: 0.6496 (mp10) outliers start: 10 outliers final: 6 residues processed: 101 average time/residue: 0.1008 time to fit residues: 14.4326 Evaluate side-chains 105 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 TYR 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: 0.5980 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 46 optimal weight: 0.0870 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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: 0.6580 moved from start: 0.3592 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= 0.228 Angle : 0.554 6.343 5799 Z= 0.303 Chirality : 0.040 0.159 658 Planarity : 0.004 0.037 712 Dihedral : 4.545 20.615 568 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.99 % Allowed : 13.05 % Favored : 84.96 % 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: 2.27 (0.39), residues: 510 helix: 2.15 (0.25), residues: 400 sheet: None (None), residues: 0 loop : -0.98 (0.72), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 102 HIS 0.005 0.001 HIS B 122 PHE 0.012 0.001 PHE B 133 TYR 0.007 0.001 TYR A 88 ARG 0.002 0.000 ARG B 53 *********************** 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 106 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8402 (tp) cc_final: 0.8147 (mm) REVERT: A 49 GLU cc_start: 0.7369 (tm-30) cc_final: 0.6760 (tm-30) REVERT: A 56 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7081 (tt) REVERT: A 74 GLN cc_start: 0.7069 (mp10) cc_final: 0.6232 (mp10) REVERT: A 279 MET cc_start: 0.4361 (ttt) cc_final: 0.3526 (ttm) REVERT: B 31 LEU cc_start: 0.8430 (tp) cc_final: 0.8173 (mm) REVERT: B 56 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7137 (tt) outliers start: 9 outliers final: 6 residues processed: 99 average time/residue: 0.0975 time to fit residues: 13.7240 Evaluate side-chains 102 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 32 optimal weight: 0.0980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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: 0.6553 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4276 Z= 0.210 Angle : 0.566 9.121 5799 Z= 0.304 Chirality : 0.040 0.173 658 Planarity : 0.004 0.032 712 Dihedral : 4.449 20.270 568 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.77 % Allowed : 13.72 % Favored : 84.51 % 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: 2.33 (0.39), residues: 510 helix: 2.15 (0.26), residues: 404 sheet: None (None), residues: 0 loop : -0.87 (0.74), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 100 HIS 0.004 0.000 HIS B 122 PHE 0.013 0.001 PHE B 133 TYR 0.011 0.001 TYR B 30 ARG 0.001 0.000 ARG B 62 *********************** 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 106 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8323 (tp) cc_final: 0.8056 (mm) REVERT: A 56 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7295 (tp) REVERT: A 74 GLN cc_start: 0.7022 (mp10) cc_final: 0.6383 (mp10) REVERT: A 279 MET cc_start: 0.4371 (ttt) cc_final: 0.3555 (ttm) REVERT: B 31 LEU cc_start: 0.8438 (tp) cc_final: 0.8193 (mm) REVERT: B 56 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7104 (tt) outliers start: 8 outliers final: 6 residues processed: 100 average time/residue: 0.0981 time to fit residues: 13.8872 Evaluate side-chains 101 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 TYR 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: 0.8980 chunk 37 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 0.0020 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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: 0.6591 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 4276 Z= 0.254 Angle : 0.605 10.599 5799 Z= 0.321 Chirality : 0.042 0.214 658 Planarity : 0.004 0.032 712 Dihedral : 4.483 21.489 568 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.55 % Allowed : 16.15 % Favored : 82.30 % 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: 2.24 (0.39), residues: 510 helix: 2.16 (0.26), residues: 400 sheet: None (None), residues: 0 loop : -1.11 (0.72), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 100 HIS 0.003 0.001 HIS B 122 PHE 0.012 0.002 PHE B 133 TYR 0.018 0.002 TYR B 30 ARG 0.001 0.000 ARG B 53 *********************** 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 102 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8431 (tp) cc_final: 0.8148 (mm) REVERT: A 56 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7097 (tt) REVERT: A 74 GLN cc_start: 0.7022 (mp10) cc_final: 0.6222 (mp10) REVERT: A 231 TYR cc_start: 0.6498 (m-80) cc_final: 0.5951 (m-80) REVERT: A 279 MET cc_start: 0.4242 (ttt) cc_final: 0.3441 (ttm) REVERT: B 31 LEU cc_start: 0.8582 (tp) cc_final: 0.8141 (mm) REVERT: B 56 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7068 (tt) REVERT: B 231 TYR cc_start: 0.6447 (m-80) cc_final: 0.6032 (m-80) outliers start: 7 outliers final: 5 residues processed: 97 average time/residue: 0.1013 time to fit residues: 13.9001 Evaluate side-chains 99 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.0970 chunk 42 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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: 0.6574 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 4276 Z= 0.241 Angle : 0.635 12.485 5799 Z= 0.328 Chirality : 0.042 0.225 658 Planarity : 0.004 0.033 712 Dihedral : 4.460 20.915 568 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.99 % Allowed : 16.37 % Favored : 81.64 % 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: 2.23 (0.40), residues: 510 helix: 2.17 (0.26), residues: 400 sheet: None (None), residues: 0 loop : -1.21 (0.71), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 102 HIS 0.003 0.000 HIS B 122 PHE 0.012 0.001 PHE B 133 TYR 0.014 0.002 TYR B 30 ARG 0.001 0.000 ARG B 62 *********************** 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 105 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8488 (tp) cc_final: 0.8105 (mm) REVERT: A 56 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7090 (tt) REVERT: A 74 GLN cc_start: 0.7007 (mp10) cc_final: 0.6207 (mp10) REVERT: A 231 TYR cc_start: 0.6621 (m-80) cc_final: 0.6003 (m-80) REVERT: A 279 MET cc_start: 0.4212 (ttt) cc_final: 0.3461 (ttm) REVERT: B 31 LEU cc_start: 0.8552 (tp) cc_final: 0.8143 (mm) REVERT: B 56 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7146 (tt) REVERT: B 74 GLN cc_start: 0.7072 (mp10) cc_final: 0.6264 (mp10) REVERT: B 231 TYR cc_start: 0.6485 (m-80) cc_final: 0.5943 (m-80) outliers start: 9 outliers final: 6 residues processed: 98 average time/residue: 0.1022 time to fit residues: 14.1643 Evaluate side-chains 102 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.0370 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 0.0980 chunk 42 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 overall best weight: 0.3458 ------------------------------------------------------------------------------- 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: 0.6521 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 4276 Z= 0.217 Angle : 0.642 13.093 5799 Z= 0.325 Chirality : 0.041 0.221 658 Planarity : 0.004 0.033 712 Dihedral : 4.356 20.496 568 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.11 % Allowed : 17.70 % Favored : 81.19 % 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: 2.35 (0.39), residues: 510 helix: 2.23 (0.26), residues: 402 sheet: None (None), residues: 0 loop : -1.09 (0.70), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 102 HIS 0.004 0.000 HIS B 122 PHE 0.013 0.001 PHE B 133 TYR 0.016 0.001 TYR A 30 ARG 0.001 0.000 ARG B 62 ********************** 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 104 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.6875 (tt) REVERT: A 74 GLN cc_start: 0.6951 (mp10) cc_final: 0.6198 (mp10) REVERT: A 231 TYR cc_start: 0.6605 (m-80) cc_final: 0.5879 (m-80) REVERT: A 279 MET cc_start: 0.4109 (ttt) cc_final: 0.3405 (ttm) REVERT: B 31 LEU cc_start: 0.8335 (tp) cc_final: 0.8104 (mm) REVERT: B 56 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7049 (tt) REVERT: B 74 GLN cc_start: 0.7043 (mp10) cc_final: 0.6222 (mp10) REVERT: B 231 TYR cc_start: 0.6668 (m-80) cc_final: 0.6037 (m-80) REVERT: B 276 PHE cc_start: 0.7380 (t80) cc_final: 0.7027 (t80) outliers start: 5 outliers final: 3 residues processed: 101 average time/residue: 0.0984 time to fit residues: 14.0736 Evaluate side-chains 101 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 56 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 9.9990 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 34 optimal weight: 0.3980 chunk 2 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.0570 chunk 30 optimal weight: 0.6980 overall best weight: 0.4098 ------------------------------------------------------------------------------- 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 = 0.4626 r_free = 0.4626 target = 0.226703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.178395 restraints weight = 5269.855| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.70 r_work: 0.3983 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.4304 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= 0.229 Angle : 0.639 12.869 5799 Z= 0.326 Chirality : 0.041 0.209 658 Planarity : 0.004 0.033 712 Dihedral : 4.323 20.308 568 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.33 % Allowed : 17.70 % Favored : 80.97 % 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: 2.28 (0.39), residues: 510 helix: 2.18 (0.26), residues: 402 sheet: None (None), residues: 0 loop : -1.13 (0.69), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 100 HIS 0.004 0.000 HIS B 122 PHE 0.013 0.001 PHE B 133 TYR 0.014 0.001 TYR A 30 ARG 0.001 0.000 ARG B 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1216.30 seconds wall clock time: 23 minutes 4.21 seconds (1384.21 seconds total)