Starting phenix.real_space_refine on Sat Apr 26 16:07:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x63_38078/04_2025/8x63_38078.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x63_38078/04_2025/8x63_38078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x63_38078/04_2025/8x63_38078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x63_38078/04_2025/8x63_38078.map" model { file = "/net/cci-nas-00/data/ceres_data/8x63_38078/04_2025/8x63_38078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x63_38078/04_2025/8x63_38078.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.056 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: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 1509 2.51 5 N 366 2.21 5 O 357 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 2252 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2231 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain breaks: 2 Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'Y5E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.23, per 1000 atoms: 0.99 Number of scatterers: 2252 At special positions: 0 Unit cell: (50.29, 75.97, 71.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 357 8.00 N 366 7.00 C 1509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 441 " - pdb=" SG CYS B 444 " 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: 0.66 Conformation dependent library (CDL) restraints added in 257.7 milliseconds 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 524 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 0 sheets defined 86.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 27 through 55 removed outlier: 3.715A pdb=" N VAL B 33 " --> pdb=" O PRO B 29 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR B 36 " --> pdb=" O VAL B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 90 Proline residue: B 82 - end of helix Processing helix chain 'B' and resid 96 through 129 removed outlier: 3.537A pdb=" N CYS B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N PHE B 119 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 164 Proline residue: B 161 - end of helix removed outlier: 3.908A pdb=" N GLY B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 186 removed outlier: 3.534A pdb=" N TYR B 185 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASP B 186 " --> pdb=" O ASP B 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 182 through 186' Processing helix chain 'B' and resid 187 through 221 removed outlier: 3.949A pdb=" N LYS B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 409 through 427 Processing helix chain 'B' and resid 428 through 441 removed outlier: 3.521A pdb=" N ALA B 439 " --> pdb=" O PHE B 435 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE B 440 " --> pdb=" O MET B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 445 removed outlier: 3.832A pdb=" N CYS B 445 " --> pdb=" O LYS B 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 442 through 445' Processing helix chain 'B' and resid 446 through 472 Proline residue: B 465 - end of helix Proline residue: B 469 - end of helix removed outlier: 4.076A pdb=" N ASN B 472 " --> pdb=" O TYR B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 481 removed outlier: 4.135A pdb=" N LYS B 476 " --> pdb=" O ASN B 472 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG B 481 " --> pdb=" O LYS B 477 " (cutoff:3.500A) 161 hydrogen bonds defined for protein. 483 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: 0.56 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 314 1.29 - 1.42: 669 1.42 - 1.55: 1299 1.55 - 1.68: 2 1.68 - 1.81: 31 Bond restraints: 2315 Sorted by residual: bond pdb=" C PHE B 424 " pdb=" N ILE B 425 " ideal model delta sigma weight residual 1.331 1.246 0.085 1.42e-02 4.96e+03 3.60e+01 bond pdb=" C ILE B 115 " pdb=" O ILE B 115 " ideal model delta sigma weight residual 1.236 1.170 0.066 1.19e-02 7.06e+03 3.09e+01 bond pdb=" C14 Y5E B 601 " pdb=" N08 Y5E B 601 " ideal model delta sigma weight residual 1.368 1.477 -0.109 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C PHE B 424 " pdb=" O PHE B 424 " ideal model delta sigma weight residual 1.236 1.160 0.076 1.47e-02 4.63e+03 2.65e+01 bond pdb=" N PHE B 424 " pdb=" CA PHE B 424 " ideal model delta sigma weight residual 1.457 1.509 -0.052 1.40e-02 5.10e+03 1.40e+01 ... (remaining 2310 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 2980 1.42 - 2.84: 113 2.84 - 4.26: 26 4.26 - 5.68: 14 5.68 - 7.10: 7 Bond angle restraints: 3140 Sorted by residual: angle pdb=" C PHE B 424 " pdb=" N ILE B 425 " pdb=" CA ILE B 425 " ideal model delta sigma weight residual 122.97 116.24 6.73 9.80e-01 1.04e+00 4.71e+01 angle pdb=" N VAL B 129 " pdb=" CA VAL B 129 " pdb=" C VAL B 129 " ideal model delta sigma weight residual 111.77 105.86 5.91 1.04e+00 9.25e-01 3.23e+01 angle pdb=" O ALA B 423 " pdb=" C ALA B 423 " pdb=" N PHE B 424 " ideal model delta sigma weight residual 122.07 116.28 5.79 1.03e+00 9.43e-01 3.16e+01 angle pdb=" CA ALA B 423 " pdb=" C ALA B 423 " pdb=" N PHE B 424 " ideal model delta sigma weight residual 117.07 122.70 -5.63 1.14e+00 7.69e-01 2.44e+01 angle pdb=" O SER B 114 " pdb=" C SER B 114 " pdb=" N ILE B 115 " ideal model delta sigma weight residual 122.03 116.85 5.18 1.08e+00 8.57e-01 2.30e+01 ... (remaining 3135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 1183 16.56 - 33.12: 136 33.12 - 49.68: 32 49.68 - 66.24: 6 66.24 - 82.80: 3 Dihedral angle restraints: 1360 sinusoidal: 555 harmonic: 805 Sorted by residual: dihedral pdb=" N PHE B 424 " pdb=" C PHE B 424 " pdb=" CA PHE B 424 " pdb=" CB PHE B 424 " ideal model delta harmonic sigma weight residual 122.80 135.14 -12.34 0 2.50e+00 1.60e-01 2.44e+01 dihedral pdb=" C PHE B 424 " pdb=" N PHE B 424 " pdb=" CA PHE B 424 " pdb=" CB PHE B 424 " ideal model delta harmonic sigma weight residual -122.60 -134.83 12.23 0 2.50e+00 1.60e-01 2.39e+01 dihedral pdb=" CA ILE B 115 " pdb=" C ILE B 115 " pdb=" N PHE B 116 " pdb=" CA PHE B 116 " ideal model delta harmonic sigma weight residual 180.00 158.22 21.78 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 1357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 346 0.098 - 0.196: 9 0.196 - 0.293: 0 0.293 - 0.391: 0 0.391 - 0.488: 2 Chirality restraints: 357 Sorted by residual: chirality pdb=" CA PHE B 424 " pdb=" N PHE B 424 " pdb=" C PHE B 424 " pdb=" CB PHE B 424 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.96e+00 chirality pdb=" CA ILE B 115 " pdb=" N ILE B 115 " pdb=" C ILE B 115 " pdb=" CB ILE B 115 " both_signs ideal model delta sigma weight residual False 2.43 2.02 0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" CA VAL B 129 " pdb=" N VAL B 129 " pdb=" C VAL B 129 " pdb=" CB VAL B 129 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 354 not shown) Planarity restraints: 371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 424 " 0.023 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C PHE B 424 " -0.079 2.00e-02 2.50e+03 pdb=" O PHE B 424 " 0.030 2.00e-02 2.50e+03 pdb=" N ILE B 425 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 114 " -0.019 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C SER B 114 " 0.062 2.00e-02 2.50e+03 pdb=" O SER B 114 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE B 115 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 115 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C ILE B 115 " -0.061 2.00e-02 2.50e+03 pdb=" O ILE B 115 " 0.022 2.00e-02 2.50e+03 pdb=" N PHE B 116 " 0.021 2.00e-02 2.50e+03 ... (remaining 368 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 881 2.91 - 3.41: 2385 3.41 - 3.90: 3516 3.90 - 4.40: 3884 4.40 - 4.90: 6390 Nonbonded interactions: 17056 Sorted by model distance: nonbonded pdb=" O PHE B 424 " pdb=" CG PHE B 424 " model vdw 2.411 3.260 nonbonded pdb=" O ASN B 408 " pdb=" N ARG B 411 " model vdw 2.513 3.120 nonbonded pdb=" O HIS B 450 " pdb=" OG1 THR B 453 " model vdw 2.516 3.040 nonbonded pdb=" O PHE B 424 " pdb=" CD1 PHE B 424 " model vdw 2.519 3.340 nonbonded pdb=" CG2 ILE B 115 " pdb=" CD1 ILE B 115 " model vdw 2.520 3.104 ... (remaining 17051 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.880 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1172 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 : 0.006 0.109 2317 Z= 0.341 Angle : 0.773 7.099 3144 Z= 0.459 Chirality : 0.055 0.488 357 Planarity : 0.007 0.051 371 Dihedral : 15.286 82.798 830 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.81 % Allowed : 0.41 % Favored : 98.78 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.52), residues: 264 helix: 1.06 (0.37), residues: 196 sheet: None (None), residues: 0 loop : -3.58 (0.62), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 165 HIS 0.009 0.002 HIS B 59 PHE 0.027 0.002 PHE B 435 TYR 0.011 0.001 TYR B 214 ARG 0.007 0.001 ARG B 481 Details of bonding type rmsd hydrogen bonds : bond 0.13054 ( 161) hydrogen bonds : angle 5.80917 ( 483) SS BOND : bond 0.00253 ( 2) SS BOND : angle 0.52317 ( 4) covalent geometry : bond 0.00599 ( 2315) covalent geometry : angle 0.77324 ( 3140) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.241 Fit side-chains REVERT: B 45 ASN cc_start: 0.2777 (m-40) cc_final: 0.2053 (m110) outliers start: 2 outliers final: 1 residues processed: 27 average time/residue: 0.1449 time to fit residues: 4.8603 Evaluate side-chains 18 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.1980 chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.0980 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 0.0870 chunk 8 optimal weight: 0.1980 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 24 optimal weight: 0.6980 overall best weight: 0.1758 ------------------------------------------------------------------------------- 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 = 0.4479 r_free = 0.4479 target = 0.223759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.189803 restraints weight = 2471.115| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 3.49 r_work: 0.4004 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1688 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2317 Z= 0.179 Angle : 0.692 7.627 3144 Z= 0.357 Chirality : 0.043 0.138 357 Planarity : 0.006 0.056 371 Dihedral : 4.911 20.563 308 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.41 % Allowed : 8.94 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.52), residues: 264 helix: 1.07 (0.36), residues: 209 sheet: None (None), residues: 0 loop : -4.12 (0.64), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 93 HIS 0.002 0.001 HIS B 59 PHE 0.012 0.001 PHE B 424 TYR 0.008 0.001 TYR B 50 ARG 0.002 0.000 ARG B 97 Details of bonding type rmsd hydrogen bonds : bond 0.05502 ( 161) hydrogen bonds : angle 4.80433 ( 483) SS BOND : bond 0.00378 ( 2) SS BOND : angle 0.54011 ( 4) covalent geometry : bond 0.00348 ( 2315) covalent geometry : angle 0.69251 ( 3140) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.244 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.1116 time to fit residues: 2.7695 Evaluate side-chains 18 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 0.0670 chunk 26 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 chunk 0 optimal weight: 0.7980 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.254350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.229529 restraints weight = 2598.788| |-----------------------------------------------------------------------------| r_work (start): 0.4631 rms_B_bonded: 3.07 r_work: 0.4488 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.4488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2421 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 2317 Z= 0.200 Angle : 0.804 9.391 3144 Z= 0.405 Chirality : 0.045 0.169 357 Planarity : 0.006 0.051 371 Dihedral : 6.134 31.363 306 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.63 % Allowed : 16.67 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.51), residues: 264 helix: 0.72 (0.36), residues: 208 sheet: None (None), residues: 0 loop : -4.11 (0.64), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP B 93 HIS 0.003 0.001 HIS B 59 PHE 0.018 0.002 PHE B 432 TYR 0.008 0.002 TYR B 87 ARG 0.003 0.001 ARG B 409 Details of bonding type rmsd hydrogen bonds : bond 0.05353 ( 161) hydrogen bonds : angle 5.01664 ( 483) SS BOND : bond 0.00233 ( 2) SS BOND : angle 0.35174 ( 4) covalent geometry : bond 0.00426 ( 2315) covalent geometry : angle 0.80465 ( 3140) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: B 56 ARG cc_start: 0.0215 (mmt90) cc_final: 0.0010 (tpt170) REVERT: B 451 MET cc_start: 0.1341 (ptp) cc_final: 0.0596 (mmp) outliers start: 4 outliers final: 3 residues processed: 27 average time/residue: 0.1364 time to fit residues: 4.6585 Evaluate side-chains 24 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 106 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 chunk 14 optimal weight: 0.2980 chunk 1 optimal weight: 0.0870 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 8 optimal weight: 0.0970 chunk 19 optimal weight: 0.1980 overall best weight: 0.1756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.240604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.213210 restraints weight = 2563.455| |-----------------------------------------------------------------------------| r_work (start): 0.4410 rms_B_bonded: 3.33 r_work: 0.4243 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2822 moved from start: 0.6536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2317 Z= 0.151 Angle : 0.671 6.689 3144 Z= 0.344 Chirality : 0.044 0.256 357 Planarity : 0.005 0.044 371 Dihedral : 5.026 18.822 306 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.44 % Allowed : 21.95 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.51), residues: 264 helix: 0.96 (0.35), residues: 208 sheet: None (None), residues: 0 loop : -4.67 (0.56), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 455 HIS 0.003 0.001 HIS B 59 PHE 0.007 0.001 PHE B 432 TYR 0.006 0.001 TYR B 214 ARG 0.002 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04980 ( 161) hydrogen bonds : angle 4.44315 ( 483) SS BOND : bond 0.00242 ( 2) SS BOND : angle 0.40759 ( 4) covalent geometry : bond 0.00311 ( 2315) covalent geometry : angle 0.67130 ( 3140) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.248 Fit side-chains REVERT: B 56 ARG cc_start: 0.1459 (mmt90) cc_final: 0.1073 (tpt170) REVERT: B 93 TRP cc_start: 0.4579 (t-100) cc_final: 0.3717 (t-100) REVERT: B 169 MET cc_start: 0.1057 (mmm) cc_final: -0.0016 (mtt) REVERT: B 435 PHE cc_start: 0.2774 (OUTLIER) cc_final: 0.2474 (t80) outliers start: 6 outliers final: 3 residues processed: 24 average time/residue: 0.1316 time to fit residues: 4.0460 Evaluate side-chains 22 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 435 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 chunk 7 optimal weight: 0.0000 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 19 optimal weight: 0.0870 chunk 15 optimal weight: 2.9990 overall best weight: 0.2960 ------------------------------------------------------------------------------- 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 = 0.4659 r_free = 0.4659 target = 0.244721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.215515 restraints weight = 2623.536| |-----------------------------------------------------------------------------| r_work (start): 0.4433 rms_B_bonded: 3.42 r_work: 0.4268 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3460 moved from start: 0.9156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2317 Z= 0.198 Angle : 0.783 11.155 3144 Z= 0.399 Chirality : 0.044 0.148 357 Planarity : 0.006 0.052 371 Dihedral : 5.919 24.414 306 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.07 % Allowed : 20.33 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.51), residues: 264 helix: 0.71 (0.34), residues: 217 sheet: None (None), residues: 0 loop : -4.54 (0.59), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 455 HIS 0.006 0.002 HIS B 59 PHE 0.007 0.001 PHE B 184 TYR 0.016 0.002 TYR B 468 ARG 0.005 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.05057 ( 161) hydrogen bonds : angle 4.83563 ( 483) SS BOND : bond 0.00301 ( 2) SS BOND : angle 0.20371 ( 4) covalent geometry : bond 0.00416 ( 2315) covalent geometry : angle 0.78391 ( 3140) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.249 Fit side-chains REVERT: B 56 ARG cc_start: 0.3737 (mmt90) cc_final: 0.2053 (tpt170) REVERT: B 97 ARG cc_start: 0.4815 (ttp80) cc_final: 0.4523 (ptm160) REVERT: B 169 MET cc_start: 0.3527 (mmm) cc_final: 0.3135 (mpp) REVERT: B 206 MET cc_start: 0.5249 (tmm) cc_final: 0.4815 (tmm) REVERT: B 421 MET cc_start: 0.2600 (OUTLIER) cc_final: 0.2037 (tmm) outliers start: 10 outliers final: 2 residues processed: 33 average time/residue: 0.1470 time to fit residues: 5.9043 Evaluate side-chains 25 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 421 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 2 optimal weight: 0.9980 chunk 17 optimal weight: 0.0570 chunk 21 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 0.0980 chunk 13 optimal weight: 0.0170 chunk 8 optimal weight: 0.5980 overall best weight: 0.2736 ------------------------------------------------------------------------------- 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 = 0.4655 r_free = 0.4655 target = 0.245048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.217470 restraints weight = 2586.032| |-----------------------------------------------------------------------------| r_work (start): 0.4434 rms_B_bonded: 3.21 r_work: 0.4270 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3657 moved from start: 1.0259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 2317 Z= 0.173 Angle : 0.712 10.984 3144 Z= 0.371 Chirality : 0.043 0.182 357 Planarity : 0.005 0.051 371 Dihedral : 5.440 23.426 306 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.85 % Allowed : 23.17 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.50), residues: 264 helix: 0.70 (0.34), residues: 216 sheet: None (None), residues: 0 loop : -4.21 (0.65), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 165 HIS 0.005 0.001 HIS B 59 PHE 0.012 0.001 PHE B 184 TYR 0.011 0.001 TYR B 185 ARG 0.001 0.000 ARG B 481 Details of bonding type rmsd hydrogen bonds : bond 0.04916 ( 161) hydrogen bonds : angle 4.47116 ( 483) SS BOND : bond 0.00259 ( 2) SS BOND : angle 0.25532 ( 4) covalent geometry : bond 0.00379 ( 2315) covalent geometry : angle 0.71289 ( 3140) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.249 Fit side-chains REVERT: B 56 ARG cc_start: 0.4316 (mmt90) cc_final: 0.2911 (tpt170) REVERT: B 97 ARG cc_start: 0.4856 (ttp80) cc_final: 0.4456 (ptm160) REVERT: B 169 MET cc_start: 0.3995 (mmm) cc_final: 0.2857 (mpp) outliers start: 7 outliers final: 5 residues processed: 27 average time/residue: 0.1517 time to fit residues: 5.0341 Evaluate side-chains 24 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 201 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 5 optimal weight: 0.0570 chunk 20 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.255840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.224232 restraints weight = 2735.734| |-----------------------------------------------------------------------------| r_work (start): 0.4481 rms_B_bonded: 3.53 r_work: 0.4339 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3930 moved from start: 1.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 2317 Z= 0.219 Angle : 0.812 7.113 3144 Z= 0.430 Chirality : 0.049 0.197 357 Planarity : 0.006 0.055 371 Dihedral : 6.332 29.756 306 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.25 % Allowed : 25.61 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.49), residues: 264 helix: 0.51 (0.34), residues: 205 sheet: None (None), residues: 0 loop : -4.27 (0.60), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP B 93 HIS 0.008 0.002 HIS B 59 PHE 0.013 0.002 PHE B 432 TYR 0.015 0.002 TYR B 138 ARG 0.003 0.001 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.05397 ( 161) hydrogen bonds : angle 5.04641 ( 483) SS BOND : bond 0.00510 ( 2) SS BOND : angle 0.75654 ( 4) covalent geometry : bond 0.00468 ( 2315) covalent geometry : angle 0.81229 ( 3140) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.239 Fit side-chains REVERT: B 53 ARG cc_start: 0.5098 (tpt170) cc_final: 0.4817 (tpt90) REVERT: B 81 MET cc_start: 0.1178 (ttt) cc_final: 0.0266 (mtp) REVERT: B 90 MET cc_start: 0.6385 (tpt) cc_final: 0.6098 (tmm) REVERT: B 421 MET cc_start: 0.3586 (tpp) cc_final: 0.3291 (tmm) outliers start: 8 outliers final: 5 residues processed: 32 average time/residue: 0.1383 time to fit residues: 5.3963 Evaluate side-chains 29 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 429 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 16 optimal weight: 0.0770 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.0570 chunk 4 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.3056 ------------------------------------------------------------------------------- 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 = 0.4764 r_free = 0.4764 target = 0.249033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.217829 restraints weight = 2623.436| |-----------------------------------------------------------------------------| r_work (start): 0.4473 rms_B_bonded: 3.09 r_work: 0.4323 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4010 moved from start: 1.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2317 Z= 0.164 Angle : 0.685 6.885 3144 Z= 0.357 Chirality : 0.043 0.167 357 Planarity : 0.005 0.059 371 Dihedral : 5.682 25.476 306 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.63 % Allowed : 26.02 % Favored : 72.36 % 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: -0.43 (0.50), residues: 264 helix: 0.64 (0.34), residues: 212 sheet: None (None), residues: 0 loop : -4.15 (0.65), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 189 HIS 0.005 0.002 HIS B 59 PHE 0.008 0.001 PHE B 190 TYR 0.010 0.001 TYR B 138 ARG 0.002 0.000 ARG B 97 Details of bonding type rmsd hydrogen bonds : bond 0.04699 ( 161) hydrogen bonds : angle 4.60641 ( 483) SS BOND : bond 0.00372 ( 2) SS BOND : angle 1.22030 ( 4) covalent geometry : bond 0.00327 ( 2315) covalent geometry : angle 0.68443 ( 3140) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.265 Fit side-chains REVERT: B 53 ARG cc_start: 0.4960 (tpt170) cc_final: 0.4421 (tpt90) REVERT: B 81 MET cc_start: 0.1475 (ttt) cc_final: 0.0698 (mtm) REVERT: B 83 MET cc_start: 0.2782 (tmm) cc_final: 0.2411 (ttp) REVERT: B 206 MET cc_start: 0.4178 (tmm) cc_final: 0.3576 (tmm) REVERT: B 421 MET cc_start: 0.3576 (tpp) cc_final: 0.3243 (tmm) outliers start: 4 outliers final: 4 residues processed: 30 average time/residue: 0.1701 time to fit residues: 6.2586 Evaluate side-chains 29 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 429 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 0.0570 chunk 6 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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 = 0.4732 r_free = 0.4732 target = 0.248490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.215203 restraints weight = 2563.213| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 3.31 r_work: 0.4214 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4261 moved from start: 1.6678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 2317 Z= 0.222 Angle : 0.808 8.814 3144 Z= 0.431 Chirality : 0.048 0.176 357 Planarity : 0.006 0.060 371 Dihedral : 6.148 25.465 306 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.85 % Allowed : 24.80 % Favored : 72.36 % 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: -0.54 (0.49), residues: 264 helix: 0.75 (0.34), residues: 202 sheet: None (None), residues: 0 loop : -4.17 (0.60), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 165 HIS 0.008 0.002 HIS B 59 PHE 0.011 0.002 PHE B 119 TYR 0.021 0.002 TYR B 431 ARG 0.005 0.001 ARG B 97 Details of bonding type rmsd hydrogen bonds : bond 0.04926 ( 161) hydrogen bonds : angle 4.85736 ( 483) SS BOND : bond 0.00521 ( 2) SS BOND : angle 1.12423 ( 4) covalent geometry : bond 0.00474 ( 2315) covalent geometry : angle 0.80717 ( 3140) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.236 Fit side-chains REVERT: B 53 ARG cc_start: 0.5168 (tpt170) cc_final: 0.4839 (tpt90) REVERT: B 55 GLU cc_start: 0.5848 (tp30) cc_final: 0.4819 (tt0) REVERT: B 81 MET cc_start: 0.2265 (ttt) cc_final: 0.1625 (mtt) REVERT: B 83 MET cc_start: 0.3413 (tmm) cc_final: 0.2860 (mtt) REVERT: B 90 MET cc_start: 0.7383 (tmm) cc_final: 0.7160 (tmm) REVERT: B 169 MET cc_start: 0.3685 (mpp) cc_final: 0.3437 (mpp) REVERT: B 206 MET cc_start: 0.4135 (tmm) cc_final: 0.3465 (tmm) REVERT: B 421 MET cc_start: 0.4291 (tpp) cc_final: 0.3884 (tmm) REVERT: B 436 MET cc_start: 0.6604 (tpp) cc_final: 0.6391 (tpp) outliers start: 7 outliers final: 7 residues processed: 32 average time/residue: 0.1471 time to fit residues: 5.7007 Evaluate side-chains 34 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 432 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 0.0070 chunk 8 optimal weight: 0.2980 chunk 14 optimal weight: 0.7980 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 = 0.4716 r_free = 0.4716 target = 0.245579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.212425 restraints weight = 2568.887| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 3.34 r_work: 0.4191 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4375 moved from start: 1.8024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2317 Z= 0.185 Angle : 0.750 8.795 3144 Z= 0.386 Chirality : 0.045 0.166 357 Planarity : 0.005 0.056 371 Dihedral : 5.890 24.729 306 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.03 % Allowed : 27.24 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.50), residues: 264 helix: 0.60 (0.35), residues: 201 sheet: None (None), residues: 0 loop : -4.04 (0.65), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 158 HIS 0.007 0.002 HIS B 59 PHE 0.013 0.001 PHE B 432 TYR 0.027 0.002 TYR B 431 ARG 0.003 0.000 ARG B 481 Details of bonding type rmsd hydrogen bonds : bond 0.04830 ( 161) hydrogen bonds : angle 4.77705 ( 483) SS BOND : bond 0.00419 ( 2) SS BOND : angle 1.83589 ( 4) covalent geometry : bond 0.00402 ( 2315) covalent geometry : angle 0.74764 ( 3140) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.245 Fit side-chains REVERT: B 55 GLU cc_start: 0.6034 (tp30) cc_final: 0.5063 (tt0) REVERT: B 81 MET cc_start: 0.2672 (ttt) cc_final: 0.2103 (mtm) REVERT: B 106 MET cc_start: 0.5380 (OUTLIER) cc_final: 0.4884 (tpp) REVERT: B 139 ARG cc_start: 0.6997 (tmm-80) cc_final: 0.6714 (tmm-80) REVERT: B 206 MET cc_start: 0.4891 (tmm) cc_final: 0.4199 (tmm) REVERT: B 421 MET cc_start: 0.4034 (tpp) cc_final: 0.3493 (tmm) outliers start: 5 outliers final: 3 residues processed: 29 average time/residue: 0.1521 time to fit residues: 5.3910 Evaluate side-chains 27 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 182 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4538 r_free = 0.4538 target = 0.226261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.189794 restraints weight = 2599.703| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 3.44 r_work: 0.4061 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4590 moved from start: 1.9771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 2317 Z= 0.219 Angle : 0.848 9.405 3144 Z= 0.446 Chirality : 0.050 0.190 357 Planarity : 0.006 0.061 371 Dihedral : 6.691 39.427 306 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 1.63 % Allowed : 27.24 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.49), residues: 264 helix: 0.45 (0.34), residues: 202 sheet: None (None), residues: 0 loop : -4.04 (0.64), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP B 93 HIS 0.010 0.002 HIS B 59 PHE 0.009 0.001 PHE B 434 TYR 0.024 0.003 TYR B 431 ARG 0.002 0.001 ARG B 481 Details of bonding type rmsd hydrogen bonds : bond 0.05514 ( 161) hydrogen bonds : angle 5.15038 ( 483) SS BOND : bond 0.00139 ( 2) SS BOND : angle 1.06539 ( 4) covalent geometry : bond 0.00497 ( 2315) covalent geometry : angle 0.84811 ( 3140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1824.11 seconds wall clock time: 31 minutes 53.11 seconds (1913.11 seconds total)