Starting phenix.real_space_refine on Thu Mar 6 00:01:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j1n_35928/03_2025/8j1n_35928.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j1n_35928/03_2025/8j1n_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_35928/03_2025/8j1n_35928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j1n_35928/03_2025/8j1n_35928.map" model { file = "/net/cci-nas-00/data/ceres_data/8j1n_35928/03_2025/8j1n_35928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j1n_35928/03_2025/8j1n_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-5624/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: 3.18, per 1000 atoms: 0.97 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: 1.02 Conformation dependent library (CDL) restraints added in 402.3 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: 0.34 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: 0.93 Time building geometry restraints manager: 1.13 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: 1.350 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.720 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: 0.010 Load rotamer database and sin/cos tables:15.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.780 ------------------------------------------------------------------------------- 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 : 0.274 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: 0.9943 time to fit residues: 70.8448 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 : 0.324 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.181713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.132785 restraints weight = 3331.273| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.73 r_work: 0.3359 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 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 0.251 506 Planarity : 0.004 0.033 569 Dihedral : 12.916 90.683 535 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 : 0.386 Fit side-chains REVERT: A 150 LYS cc_start: 0.8368 (tptp) cc_final: 0.8078 (tttm) REVERT: A 157 TYR cc_start: 0.7957 (m-80) cc_final: 0.7017 (t80) REVERT: A 169 LEU cc_start: 0.8361 (mm) cc_final: 0.8048 (mt) REVERT: B 71 SER cc_start: 0.8747 (t) cc_final: 0.8381 (t) REVERT: B 78 THR cc_start: 0.9188 (m) cc_final: 0.8879 (t) REVERT: B 83 MET cc_start: 0.8354 (mtp) cc_final: 0.8052 (mtp) REVERT: B 95 TYR cc_start: 0.8356 (m-80) cc_final: 0.7929 (m-80) REVERT: B 119 VAL cc_start: 0.7746 (OUTLIER) cc_final: 0.7488 (p) outliers start: 5 outliers final: 1 residues processed: 61 average time/residue: 1.2516 time to fit residues: 78.9653 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 : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 chunk 35 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.181399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.132714 restraints weight = 3263.511| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.67 r_work: 0.3345 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1812 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 : 0.522 6.549 4559 Z= 0.270 Chirality : 0.040 0.205 506 Planarity : 0.004 0.030 569 Dihedral : 12.218 83.299 535 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.37 % Allowed : 11.83 % Favored : 85.80 % 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: 2.59 (0.39), residues: 410 helix: 2.84 (0.32), residues: 223 sheet: 0.38 (0.64), residues: 54 loop : 0.39 (0.52), 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 59 PHE 0.018 0.002 PHE B 101 TYR 0.011 0.001 TYR A 157 ARG 0.002 0.000 ARG B 104 *********************** 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 66 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.391 Fit side-chains REVERT: A 150 LYS cc_start: 0.8370 (tptp) cc_final: 0.8121 (tttm) REVERT: A 157 TYR cc_start: 0.7890 (m-80) cc_final: 0.7035 (t80) REVERT: A 169 LEU cc_start: 0.8384 (mm) cc_final: 0.8066 (mt) REVERT: A 187 ASN cc_start: 0.8563 (t0) cc_final: 0.7818 (m-40) REVERT: B 71 SER cc_start: 0.8763 (t) cc_final: 0.8486 (t) REVERT: B 83 MET cc_start: 0.8313 (mtp) cc_final: 0.7866 (mtp) REVERT: B 95 TYR cc_start: 0.8454 (m-80) cc_final: 0.8145 (m-80) outliers start: 8 outliers final: 2 residues processed: 62 average time/residue: 1.3149 time to fit residues: 85.5356 Evaluate side-chains 57 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain B residue 93 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.179651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.130916 restraints weight = 3312.332| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.68 r_work: 0.3341 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3363 Z= 0.227 Angle : 0.541 6.448 4559 Z= 0.277 Chirality : 0.041 0.230 506 Planarity : 0.004 0.030 569 Dihedral : 12.102 80.286 535 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.37 % Allowed : 12.72 % Favored : 84.91 % 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: 2.74 (0.39), residues: 410 helix: 2.92 (0.31), residues: 223 sheet: 0.57 (0.64), residues: 54 loop : 0.47 (0.53), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 56 HIS 0.004 0.001 HIS B 59 PHE 0.011 0.002 PHE A 128 TYR 0.013 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: 8 poor density : 58 time to evaluate : 0.360 Fit side-chains REVERT: A 116 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7642 (mp) REVERT: A 150 LYS cc_start: 0.8383 (tptp) cc_final: 0.8133 (tttm) REVERT: A 157 TYR cc_start: 0.7953 (m-80) cc_final: 0.7081 (t80) REVERT: A 169 LEU cc_start: 0.8392 (mm) cc_final: 0.8080 (mt) REVERT: B 71 SER cc_start: 0.8758 (t) cc_final: 0.8209 (p) REVERT: B 95 TYR cc_start: 0.8478 (m-80) cc_final: 0.8173 (m-80) outliers start: 8 outliers final: 3 residues processed: 62 average time/residue: 1.1978 time to fit residues: 76.5685 Evaluate side-chains 61 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 116 ILE 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 38 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4002 r_free = 0.4002 target = 0.179758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.130060 restraints weight = 3337.524| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.75 r_work: 0.3329 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3363 Z= 0.230 Angle : 0.534 6.163 4559 Z= 0.272 Chirality : 0.041 0.263 506 Planarity : 0.004 0.030 569 Dihedral : 12.014 80.068 535 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.07 % Allowed : 14.50 % 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: 2.89 (0.39), residues: 410 helix: 3.03 (0.31), residues: 223 sheet: 0.68 (0.65), residues: 54 loop : 0.55 (0.53), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 56 HIS 0.004 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 B 104 *********************** 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 65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.341 Fit side-chains REVERT: A 55 LYS cc_start: 0.8413 (tptt) cc_final: 0.8008 (tmmt) REVERT: A 150 LYS cc_start: 0.8373 (tptp) cc_final: 0.8096 (tttm) REVERT: A 157 TYR cc_start: 0.7951 (m-80) cc_final: 0.7036 (t80) REVERT: A 169 LEU cc_start: 0.8367 (mm) cc_final: 0.8038 (mt) REVERT: B 71 SER cc_start: 0.8683 (t) cc_final: 0.8181 (p) REVERT: B 95 TYR cc_start: 0.8495 (m-80) cc_final: 0.8061 (m-80) outliers start: 7 outliers final: 3 residues processed: 62 average time/residue: 1.0823 time to fit residues: 69.3518 Evaluate side-chains 59 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER 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 40 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.178334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.128102 restraints weight = 3391.808| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.77 r_work: 0.3299 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3363 Z= 0.294 Angle : 0.576 6.131 4559 Z= 0.293 Chirality : 0.044 0.292 506 Planarity : 0.004 0.032 569 Dihedral : 12.196 81.463 535 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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: 2.77 (0.39), residues: 410 helix: 2.91 (0.31), residues: 222 sheet: 0.65 (0.65), residues: 54 loop : 0.55 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 56 HIS 0.005 0.001 HIS B 59 PHE 0.014 0.002 PHE A 128 TYR 0.015 0.001 TYR A 157 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 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.433 Fit side-chains REVERT: A 150 LYS cc_start: 0.8382 (tptp) cc_final: 0.8109 (tttm) REVERT: A 157 TYR cc_start: 0.8017 (m-80) cc_final: 0.7065 (t80) REVERT: B 71 SER cc_start: 0.8740 (t) cc_final: 0.8459 (t) REVERT: B 95 TYR cc_start: 0.8545 (m-80) cc_final: 0.8141 (m-80) outliers start: 7 outliers final: 3 residues processed: 60 average time/residue: 0.8872 time to fit residues: 55.4795 Evaluate side-chains 58 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER 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 1 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 10 optimal weight: 0.0060 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.181310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.132188 restraints weight = 3270.448| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.73 r_work: 0.3337 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2432 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= 0.171 Angle : 0.531 12.764 4559 Z= 0.263 Chirality : 0.042 0.377 506 Planarity : 0.004 0.032 569 Dihedral : 11.697 79.155 535 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.18 % Allowed : 16.27 % 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: 3.07 (0.40), residues: 410 helix: 3.19 (0.31), residues: 222 sheet: 0.79 (0.64), residues: 54 loop : 0.63 (0.54), 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 0.007 0.001 PHE A 128 TYR 0.009 0.001 TYR A 157 ARG 0.003 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: 4 poor density : 61 time to evaluate : 0.393 Fit side-chains REVERT: A 150 LYS cc_start: 0.8363 (tptp) cc_final: 0.8117 (tttm) REVERT: A 157 TYR cc_start: 0.7879 (m-80) cc_final: 0.7053 (t80) REVERT: A 169 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8016 (mt) REVERT: A 187 ASN cc_start: 0.8554 (t0) cc_final: 0.7804 (m-40) REVERT: B 71 SER cc_start: 0.8701 (t) cc_final: 0.8257 (p) REVERT: B 83 MET cc_start: 0.8298 (mtp) cc_final: 0.8022 (mtp) REVERT: B 95 TYR cc_start: 0.8511 (m-80) cc_final: 0.8209 (m-80) outliers start: 4 outliers final: 1 residues processed: 63 average time/residue: 0.8865 time to fit residues: 58.3210 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 : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU 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 1 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.178665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.131131 restraints weight = 3309.932| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.08 r_work: 0.3323 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3363 Z= 0.270 Angle : 0.578 11.320 4559 Z= 0.291 Chirality : 0.044 0.368 506 Planarity : 0.004 0.031 569 Dihedral : 11.854 78.620 535 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.07 % Allowed : 15.98 % Favored : 81.95 % 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: 2.90 (0.39), residues: 410 helix: 3.02 (0.31), residues: 222 sheet: 0.72 (0.64), residues: 54 loop : 0.59 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 56 HIS 0.002 0.001 HIS B 35 PHE 0.013 0.002 PHE A 223 TYR 0.014 0.001 TYR A 157 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 64 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.379 Fit side-chains REVERT: A 150 LYS cc_start: 0.8356 (tptp) cc_final: 0.8100 (tttm) REVERT: A 157 TYR cc_start: 0.7974 (m-80) cc_final: 0.7081 (t80) REVERT: A 169 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8059 (mt) REVERT: B 71 SER cc_start: 0.8694 (t) cc_final: 0.8180 (p) REVERT: B 95 TYR cc_start: 0.8557 (m-80) cc_final: 0.8218 (m-80) outliers start: 7 outliers final: 4 residues processed: 59 average time/residue: 1.3968 time to fit residues: 84.7266 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 : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 169 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.4002 r_free = 0.4002 target = 0.180037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.133061 restraints weight = 3350.156| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.02 r_work: 0.3326 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2523 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= 0.202 Angle : 0.547 12.061 4559 Z= 0.272 Chirality : 0.042 0.377 506 Planarity : 0.004 0.031 569 Dihedral : 11.659 76.611 535 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.18 % Allowed : 17.46 % 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: 3.03 (0.39), residues: 410 helix: 3.16 (0.31), residues: 222 sheet: 0.80 (0.64), residues: 54 loop : 0.58 (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 0.010 0.001 PHE A 128 TYR 0.012 0.001 TYR A 157 ARG 0.002 0.000 ARG B 104 *********************** 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 65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.329 Fit side-chains REVERT: A 150 LYS cc_start: 0.8354 (tptp) cc_final: 0.8116 (tttp) REVERT: A 157 TYR cc_start: 0.7959 (m-80) cc_final: 0.7105 (t80) REVERT: A 169 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8028 (mt) REVERT: B 71 SER cc_start: 0.8684 (t) cc_final: 0.8213 (p) REVERT: B 95 TYR cc_start: 0.8522 (m-80) cc_final: 0.8103 (m-80) outliers start: 4 outliers final: 3 residues processed: 62 average time/residue: 0.8575 time to fit residues: 55.3746 Evaluate side-chains 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 215 LEU 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 24 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.178395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.128846 restraints weight = 3265.665| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.72 r_work: 0.3312 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3363 Z= 0.276 Angle : 0.588 11.346 4559 Z= 0.294 Chirality : 0.044 0.364 506 Planarity : 0.004 0.030 569 Dihedral : 11.869 76.795 535 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.07 % Allowed : 17.16 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.39), residues: 410 helix: 2.99 (0.31), residues: 222 sheet: 0.74 (0.64), residues: 54 loop : 0.51 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 56 HIS 0.003 0.001 HIS B 59 PHE 0.013 0.002 PHE A 223 TYR 0.014 0.001 TYR A 157 ARG 0.003 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 65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.357 Fit side-chains REVERT: A 70 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7302 (ttm-80) REVERT: A 150 LYS cc_start: 0.8351 (tptp) cc_final: 0.8119 (tttm) REVERT: A 157 TYR cc_start: 0.7987 (m-80) cc_final: 0.7111 (t80) REVERT: B 71 SER cc_start: 0.8739 (t) cc_final: 0.8196 (p) REVERT: B 95 TYR cc_start: 0.8580 (m-80) cc_final: 0.8242 (m-80) outliers start: 7 outliers final: 3 residues processed: 60 average time/residue: 0.9141 time to fit residues: 57.1398 Evaluate side-chains 61 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 69 THR 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 26 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 0.0870 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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 = 0.179722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.130494 restraints weight = 3290.688| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.72 r_work: 0.3332 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2582 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= 0.199 Angle : 0.551 11.610 4559 Z= 0.273 Chirality : 0.042 0.358 506 Planarity : 0.004 0.031 569 Dihedral : 11.686 76.346 535 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 : 0.89 % Allowed : 18.64 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.39), residues: 410 helix: 3.14 (0.31), residues: 222 sheet: 0.79 (0.64), residues: 54 loop : 0.52 (0.53), 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 35 PHE 0.010 0.001 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: 3610.08 seconds wall clock time: 64 minutes 45.00 seconds (3885.00 seconds total)