Starting phenix.real_space_refine on Fri Dec 27 10:27:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j1n_35928/12_2024/8j1n_35928.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j1n_35928/12_2024/8j1n_35928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j1n_35928/12_2024/8j1n_35928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j1n_35928/12_2024/8j1n_35928.map" model { file = "/net/cci-nas-00/data/ceres_data/8j1n_35928/12_2024/8j1n_35928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j1n_35928/12_2024/8j1n_35928.cif" } resolution = 2.51 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= -0.001 sd= 0.146 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 P 4 5.49 5 S 18 5.16 5 C 2106 2.51 5 N 545 2.21 5 O 619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3292 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2180 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 274} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 997 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "A" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 115 Unusual residues: {'CDL': 1, 'DNF': 1, 'PC1': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 102 Time building chain proxies: 3.07, per 1000 atoms: 0.93 Number of scatterers: 3292 At special positions: 0 Unit cell: (66.72, 68.388, 110.922, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 4 15.00 O 619 8.00 N 545 7.00 C 2106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.15 Conformation dependent library (CDL) restraints added in 419.5 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 754 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 3 sheets defined 62.6% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 11 through 43 Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 56 through 69 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 76 through 107 removed outlier: 4.129A pdb=" N PHE A 101 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 143 removed outlier: 3.512A pdb=" N LYS A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 155 through 168 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.603A pdb=" N LYS A 174 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 205 Processing helix chain 'A' and resid 210 through 242 removed outlier: 3.839A pdb=" N HIS A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Proline residue: A 231 - end of helix Processing helix chain 'A' and resid 249 through 262 Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.655A pdb=" N LYS A 268 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 297 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.727A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.727A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) 234 hydrogen bonds defined for protein. 648 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: 1.00 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 517 1.30 - 1.43: 891 1.43 - 1.56: 1920 1.56 - 1.69: 8 1.69 - 1.81: 27 Bond restraints: 3363 Sorted by residual: bond pdb=" CA7 CDL A 402 " pdb=" OA8 CDL A 402 " ideal model delta sigma weight residual 1.334 1.457 -0.123 1.10e-02 8.26e+03 1.26e+02 bond pdb=" CB7 CDL A 402 " pdb=" OB8 CDL A 402 " ideal model delta sigma weight residual 1.334 1.442 -0.108 1.10e-02 8.26e+03 9.61e+01 bond pdb=" CA5 CDL A 402 " pdb=" OA6 CDL A 402 " ideal model delta sigma weight residual 1.342 1.458 -0.116 1.50e-02 4.44e+03 5.93e+01 bond pdb=" CB5 CDL A 402 " pdb=" OB6 CDL A 402 " ideal model delta sigma weight residual 1.342 1.445 -0.103 1.50e-02 4.44e+03 4.74e+01 bond pdb=" C21 PC1 A 403 " pdb=" O21 PC1 A 403 " ideal model delta sigma weight residual 1.331 1.457 -0.126 2.00e-02 2.50e+03 3.96e+01 ... (remaining 3358 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 4345 1.95 - 3.90: 144 3.90 - 5.85: 55 5.85 - 7.80: 6 7.80 - 9.75: 9 Bond angle restraints: 4559 Sorted by residual: angle pdb=" C51 CDL A 402 " pdb=" CB5 CDL A 402 " pdb=" OB6 CDL A 402 " ideal model delta sigma weight residual 111.33 120.79 -9.46 1.32e+00 5.72e-01 5.12e+01 angle pdb=" C11 CDL A 402 " pdb=" CA5 CDL A 402 " pdb=" OA6 CDL A 402 " ideal model delta sigma weight residual 111.33 120.58 -9.25 1.32e+00 5.72e-01 4.90e+01 angle pdb=" C71 CDL A 402 " pdb=" CB7 CDL A 402 " pdb=" OB8 CDL A 402 " ideal model delta sigma weight residual 111.64 121.39 -9.75 1.65e+00 3.69e-01 3.51e+01 angle pdb=" C31 CDL A 402 " pdb=" CA7 CDL A 402 " pdb=" OA8 CDL A 402 " ideal model delta sigma weight residual 111.64 120.78 -9.14 1.65e+00 3.69e-01 3.08e+01 angle pdb=" OB6 CDL A 402 " pdb=" CB5 CDL A 402 " pdb=" OB7 CDL A 402 " ideal model delta sigma weight residual 123.92 118.75 5.17 1.00e+00 9.92e-01 2.65e+01 ... (remaining 4554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.92: 1835 20.92 - 41.84: 122 41.84 - 62.75: 34 62.75 - 83.67: 4 83.67 - 104.59: 4 Dihedral angle restraints: 1999 sinusoidal: 816 harmonic: 1183 Sorted by residual: dihedral pdb=" CA ARG B 72 " pdb=" C ARG B 72 " pdb=" N ASP B 73 " pdb=" CA ASP B 73 " ideal model delta harmonic sigma weight residual 180.00 155.64 24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA5 CDL A 402 " pdb=" CA4 CDL A 402 " pdb=" OA6 CDL A 402 " pdb=" CA6 CDL A 402 " ideal model delta sinusoidal sigma weight residual 168.24 63.65 104.59 1 3.00e+01 1.11e-03 1.34e+01 dihedral pdb=" CA TRP B 111 " pdb=" C TRP B 111 " pdb=" N GLY B 112 " pdb=" CA GLY B 112 " ideal model delta harmonic sigma weight residual 180.00 163.83 16.17 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 1996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 337 0.045 - 0.090: 132 0.090 - 0.135: 33 0.135 - 0.180: 3 0.180 - 0.225: 1 Chirality restraints: 506 Sorted by residual: chirality pdb=" CB ILE A 116 " pdb=" CA ILE A 116 " pdb=" CG1 ILE A 116 " pdb=" CG2 ILE A 116 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA VAL A 211 " pdb=" N VAL A 211 " pdb=" C VAL A 211 " pdb=" CB VAL A 211 " both_signs ideal model delta sigma weight residual False 2.44 2.30 0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CG LEU A 90 " pdb=" CB LEU A 90 " pdb=" CD1 LEU A 90 " pdb=" CD2 LEU A 90 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 503 not shown) Planarity restraints: 569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 101 " 0.025 2.00e-02 2.50e+03 3.82e-02 2.55e+01 pdb=" CG PHE B 101 " -0.086 2.00e-02 2.50e+03 pdb=" CD1 PHE B 101 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 PHE B 101 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE B 101 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B 101 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 101 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 27 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO B 28 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 28 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 28 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 96 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.82e+00 pdb=" C ASP A 96 " 0.023 2.00e-02 2.50e+03 pdb=" O ASP A 96 " -0.009 2.00e-02 2.50e+03 pdb=" N THR A 97 " -0.008 2.00e-02 2.50e+03 ... (remaining 566 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 501 2.76 - 3.29: 3101 3.29 - 3.83: 5992 3.83 - 4.36: 6913 4.36 - 4.90: 11952 Nonbonded interactions: 28459 Sorted by model distance: nonbonded pdb=" O TRP A 173 " pdb=" OG1 THR A 176 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR A 30 " pdb=" NH1 ARG A 276 " model vdw 2.233 3.120 nonbonded pdb=" O GLY A 130 " pdb=" OG1 THR A 133 " model vdw 2.300 3.040 nonbonded pdb=" O ALA A 63 " pdb=" OG1 THR A 67 " model vdw 2.342 3.040 nonbonded pdb=" OE2 GLU B 6 " pdb=" N CYS B 96 " model vdw 2.353 3.120 ... (remaining 28454 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.940 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 0.126 3363 Z= 0.609 Angle : 1.010 9.745 4559 Z= 0.523 Chirality : 0.049 0.225 506 Planarity : 0.005 0.038 569 Dihedral : 15.984 104.588 1242 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: 1.72 (0.39), residues: 410 helix: 1.87 (0.32), residues: 223 sheet: -0.02 (0.64), residues: 59 loop : 0.60 (0.54), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 56 HIS 0.004 0.001 HIS A 214 PHE 0.086 0.004 PHE B 101 TYR 0.020 0.002 TYR A 157 ARG 0.008 0.001 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.348 Fit side-chains REVERT: A 157 TYR cc_start: 0.7543 (m-80) cc_final: 0.6787 (t80) REVERT: A 169 LEU cc_start: 0.8127 (mm) cc_final: 0.7893 (mt) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.9980 time to fit residues: 71.3478 Evaluate side-chains 61 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.0060 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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: 0.7611 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3363 Z= 0.190 Angle : 0.553 6.671 4559 Z= 0.287 Chirality : 0.041 0.250 506 Planarity : 0.004 0.033 569 Dihedral : 12.915 90.680 535 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.48 % Allowed : 10.65 % Favored : 87.87 % 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: 410 helix: 2.58 (0.32), residues: 223 sheet: 0.01 (0.65), residues: 54 loop : 0.34 (0.51), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 111 HIS 0.003 0.001 HIS B 35 PHE 0.026 0.002 PHE B 101 TYR 0.010 0.001 TYR A 157 ARG 0.002 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.333 Fit side-chains REVERT: A 150 LYS cc_start: 0.8219 (tptp) cc_final: 0.7957 (tttm) REVERT: A 157 TYR cc_start: 0.7353 (m-80) cc_final: 0.6736 (t80) REVERT: A 169 LEU cc_start: 0.8175 (mm) cc_final: 0.7895 (mt) outliers start: 5 outliers final: 1 residues processed: 61 average time/residue: 1.0206 time to fit residues: 64.6300 Evaluate side-chains 57 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 0.0770 chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 0.0370 chunk 36 optimal weight: 0.3980 chunk 12 optimal weight: 0.1980 chunk 29 optimal weight: 6.9990 overall best weight: 0.2616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 3363 Z= 0.153 Angle : 0.496 6.532 4559 Z= 0.256 Chirality : 0.040 0.209 506 Planarity : 0.004 0.029 569 Dihedral : 12.085 83.555 535 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.78 % Allowed : 13.02 % Favored : 85.21 % 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: 2.77 (0.40), residues: 410 helix: 2.99 (0.32), residues: 223 sheet: 0.44 (0.63), residues: 54 loop : 0.49 (0.52), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 111 HIS 0.002 0.001 HIS B 35 PHE 0.013 0.001 PHE B 101 TYR 0.011 0.001 TYR B 80 ARG 0.002 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.340 Fit side-chains REVERT: A 157 TYR cc_start: 0.7230 (m-80) cc_final: 0.6726 (t80) REVERT: A 169 LEU cc_start: 0.8155 (mm) cc_final: 0.7890 (mt) REVERT: A 187 ASN cc_start: 0.8014 (t0) cc_final: 0.7354 (m-40) REVERT: A 219 LEU cc_start: 0.7982 (tp) cc_final: 0.7522 (tp) outliers start: 6 outliers final: 2 residues processed: 65 average time/residue: 0.8865 time to fit residues: 59.9873 Evaluate side-chains 58 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 33 optimal weight: 0.0030 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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: 0.7623 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3363 Z= 0.189 Angle : 0.516 6.354 4559 Z= 0.265 Chirality : 0.041 0.253 506 Planarity : 0.004 0.029 569 Dihedral : 11.918 80.045 535 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.66 % Allowed : 11.83 % Favored : 85.50 % 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: 2.94 (0.39), residues: 410 helix: 3.11 (0.31), residues: 223 sheet: 0.59 (0.63), residues: 54 loop : 0.54 (0.52), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 111 HIS 0.004 0.001 HIS B 59 PHE 0.010 0.001 PHE B 101 TYR 0.011 0.001 TYR A 157 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.421 Fit side-chains REVERT: A 157 TYR cc_start: 0.7346 (m-80) cc_final: 0.6789 (t80) REVERT: A 169 LEU cc_start: 0.8165 (mm) cc_final: 0.7892 (mt) REVERT: A 187 ASN cc_start: 0.8044 (t0) cc_final: 0.7360 (m-40) REVERT: A 219 LEU cc_start: 0.8002 (tp) cc_final: 0.7496 (tp) REVERT: A 255 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8552 (tpt) outliers start: 9 outliers final: 4 residues processed: 62 average time/residue: 1.0090 time to fit residues: 64.8707 Evaluate side-chains 62 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7638 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3363 Z= 0.205 Angle : 0.528 6.251 4559 Z= 0.268 Chirality : 0.041 0.241 506 Planarity : 0.004 0.029 569 Dihedral : 11.865 78.775 535 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.66 % Allowed : 13.91 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.40), residues: 410 helix: 3.15 (0.31), residues: 223 sheet: 0.73 (0.65), residues: 54 loop : 0.52 (0.52), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 56 HIS 0.003 0.001 HIS B 59 PHE 0.010 0.002 PHE A 128 TYR 0.012 0.001 TYR B 95 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.370 Fit side-chains REVERT: A 116 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7610 (mp) REVERT: A 157 TYR cc_start: 0.7375 (m-80) cc_final: 0.6801 (t80) REVERT: A 169 LEU cc_start: 0.8178 (mm) cc_final: 0.7907 (mt) REVERT: A 187 ASN cc_start: 0.8063 (t0) cc_final: 0.7358 (m-40) REVERT: A 255 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8519 (tpt) outliers start: 9 outliers final: 4 residues processed: 63 average time/residue: 1.0576 time to fit residues: 68.9250 Evaluate side-chains 60 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 13 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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: 0.7627 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3363 Z= 0.186 Angle : 0.518 6.995 4559 Z= 0.262 Chirality : 0.041 0.283 506 Planarity : 0.004 0.028 569 Dihedral : 11.653 78.479 535 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.07 % Allowed : 15.38 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.14 (0.40), residues: 410 helix: 3.26 (0.31), residues: 223 sheet: 0.79 (0.65), residues: 54 loop : 0.61 (0.53), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 111 HIS 0.003 0.001 HIS B 35 PHE 0.009 0.001 PHE A 201 TYR 0.014 0.001 TYR B 95 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.407 Fit side-chains REVERT: A 55 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7649 (tmtt) REVERT: A 157 TYR cc_start: 0.7290 (m-80) cc_final: 0.6770 (t80) REVERT: A 169 LEU cc_start: 0.8150 (mm) cc_final: 0.7886 (mt) REVERT: A 187 ASN cc_start: 0.8041 (t0) cc_final: 0.7366 (m-40) REVERT: A 255 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8534 (tpt) outliers start: 7 outliers final: 3 residues processed: 62 average time/residue: 0.9233 time to fit residues: 59.5566 Evaluate side-chains 61 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7632 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3363 Z= 0.193 Angle : 0.544 12.831 4559 Z= 0.271 Chirality : 0.042 0.358 506 Planarity : 0.004 0.028 569 Dihedral : 11.547 78.439 535 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.37 % Allowed : 15.98 % Favored : 81.66 % 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: 3.18 (0.40), residues: 410 helix: 3.30 (0.31), residues: 222 sheet: 0.89 (0.65), residues: 54 loop : 0.57 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 111 HIS 0.003 0.001 HIS B 35 PHE 0.009 0.001 PHE A 128 TYR 0.011 0.001 TYR A 157 ARG 0.002 0.000 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.327 Fit side-chains REVERT: A 157 TYR cc_start: 0.7299 (m-80) cc_final: 0.6771 (t80) REVERT: A 169 LEU cc_start: 0.8126 (mm) cc_final: 0.7875 (mt) REVERT: A 187 ASN cc_start: 0.8041 (t0) cc_final: 0.7362 (m-40) REVERT: A 255 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8524 (tpt) outliers start: 8 outliers final: 4 residues processed: 62 average time/residue: 0.9595 time to fit residues: 61.7971 Evaluate side-chains 60 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 35 optimal weight: 0.0010 chunk 37 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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: 0.7627 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3363 Z= 0.186 Angle : 0.530 10.389 4559 Z= 0.267 Chirality : 0.042 0.342 506 Planarity : 0.004 0.029 569 Dihedral : 11.457 77.319 535 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.96 % Allowed : 15.68 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.40), residues: 410 helix: 3.28 (0.31), residues: 222 sheet: 1.01 (0.65), residues: 54 loop : 0.63 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 111 HIS 0.003 0.001 HIS B 35 PHE 0.008 0.001 PHE A 128 TYR 0.014 0.001 TYR B 95 ARG 0.003 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.371 Fit side-chains REVERT: A 55 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7658 (tmtt) REVERT: A 157 TYR cc_start: 0.7275 (m-80) cc_final: 0.6769 (t80) REVERT: A 169 LEU cc_start: 0.8133 (mm) cc_final: 0.7866 (mt) REVERT: A 187 ASN cc_start: 0.8025 (t0) cc_final: 0.7342 (m-40) REVERT: A 255 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8527 (tpt) outliers start: 10 outliers final: 3 residues processed: 64 average time/residue: 1.0168 time to fit residues: 67.4166 Evaluate side-chains 62 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 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 214 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3363 Z= 0.218 Angle : 0.560 11.683 4559 Z= 0.280 Chirality : 0.043 0.363 506 Planarity : 0.004 0.029 569 Dihedral : 11.547 76.055 535 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.66 % Allowed : 15.68 % Favored : 81.66 % 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: 3.13 (0.39), residues: 410 helix: 3.21 (0.31), residues: 222 sheet: 1.01 (0.65), residues: 54 loop : 0.59 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 111 HIS 0.002 0.001 HIS B 59 PHE 0.011 0.002 PHE A 128 TYR 0.012 0.001 TYR A 157 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.387 Fit side-chains REVERT: A 55 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7673 (tmtt) REVERT: A 157 TYR cc_start: 0.7371 (m-80) cc_final: 0.6794 (t80) REVERT: A 169 LEU cc_start: 0.8157 (mm) cc_final: 0.7886 (mt) outliers start: 9 outliers final: 6 residues processed: 62 average time/residue: 0.9581 time to fit residues: 61.6574 Evaluate side-chains 65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 4 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 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 214 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3363 Z= 0.196 Angle : 0.546 11.701 4559 Z= 0.273 Chirality : 0.042 0.354 506 Planarity : 0.004 0.030 569 Dihedral : 11.525 74.828 535 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.78 % Allowed : 16.86 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.40), residues: 410 helix: 3.26 (0.31), residues: 222 sheet: 1.16 (0.65), residues: 54 loop : 0.60 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 111 HIS 0.003 0.001 HIS B 35 PHE 0.009 0.001 PHE A 128 TYR 0.017 0.001 TYR B 95 ARG 0.002 0.000 ARG A 161 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.388 Fit side-chains REVERT: A 55 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7683 (tmtt) REVERT: A 157 TYR cc_start: 0.7323 (m-80) cc_final: 0.6785 (t80) REVERT: A 169 LEU cc_start: 0.8150 (mm) cc_final: 0.7878 (mt) REVERT: A 187 ASN cc_start: 0.8038 (t0) cc_final: 0.7358 (m-40) outliers start: 6 outliers final: 4 residues processed: 60 average time/residue: 0.9697 time to fit residues: 60.4793 Evaluate side-chains 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.179996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.130229 restraints weight = 3264.110| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.73 r_work: 0.3323 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3363 Z= 0.217 Angle : 0.560 11.491 4559 Z= 0.281 Chirality : 0.043 0.355 506 Planarity : 0.004 0.030 569 Dihedral : 11.565 74.115 535 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.78 % Allowed : 16.86 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.40), residues: 410 helix: 3.21 (0.31), residues: 222 sheet: 1.15 (0.65), residues: 54 loop : 0.57 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 111 HIS 0.003 0.001 HIS B 35 PHE 0.011 0.002 PHE A 128 TYR 0.012 0.001 TYR A 157 ARG 0.002 0.000 ARG A 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1787.58 seconds wall clock time: 32 minutes 41.67 seconds (1961.67 seconds total)