Starting phenix.real_space_refine on Mon Jan 13 13:45:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x63_38078/01_2025/8x63_38078.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x63_38078/01_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_38078/01_2025/8x63_38078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x63_38078/01_2025/8x63_38078.map" model { file = "/net/cci-nas-00/data/ceres_data/8x63_38078/01_2025/8x63_38078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x63_38078/01_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-5571/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: 2.19, per 1000 atoms: 0.97 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: 0.62 Conformation dependent library (CDL) restraints added in 250.0 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: 0.59 Time building geometry restraints manager: 0.71 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: 0.920 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.130 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.760 ------------------------------------------------------------------------------- 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 2315 Z= 0.372 Angle : 0.773 7.099 3140 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 *********************** 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 : 0.235 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: 0.1484 time to fit residues: 4.9727 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 : 0.236 ------------------------------------------------------------------------------- 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 = 31)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.189813 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 2315 Z= 0.215 Angle : 0.693 7.627 3140 Z= 0.358 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 *********************** 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 : 0.233 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.1151 time to fit residues: 2.8367 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 : 0.228 ------------------------------------------------------------------------------- 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: 0.1980 chunk 26 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 chunk 0 optimal weight: 0.8980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 = 0.4594 r_free = 0.4594 target = 0.236631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.211083 restraints weight = 2604.820| |-----------------------------------------------------------------------------| r_work (start): 0.4387 rms_B_bonded: 3.28 r_work: 0.4229 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2837 moved from start: 0.6142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2315 Z= 0.286 Angle : 0.866 10.457 3140 Z= 0.437 Chirality : 0.049 0.172 357 Planarity : 0.006 0.052 371 Dihedral : 6.615 37.780 306 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.03 % Allowed : 17.07 % Favored : 80.89 % 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: -0.77 (0.51), residues: 264 helix: 0.44 (0.36), residues: 208 sheet: None (None), residues: 0 loop : -4.14 (0.64), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 93 HIS 0.003 0.001 HIS B 59 PHE 0.013 0.002 PHE B 432 TYR 0.011 0.002 TYR B 431 ARG 0.004 0.001 ARG B 409 *********************** 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 30 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.230 Fit side-chains REVERT: B 451 MET cc_start: 0.1895 (ptp) cc_final: 0.0945 (mmp) REVERT: B 481 ARG cc_start: 0.2474 (ttm-80) cc_final: 0.2053 (mtt180) outliers start: 5 outliers final: 3 residues processed: 28 average time/residue: 0.1564 time to fit residues: 5.3493 Evaluate side-chains 22 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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: 0.9980 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 26 optimal weight: 0.1980 chunk 14 optimal weight: 0.1980 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 0.0980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 = 0.4625 r_free = 0.4625 target = 0.240642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.212149 restraints weight = 2599.997| |-----------------------------------------------------------------------------| r_work (start): 0.4385 rms_B_bonded: 3.49 r_work: 0.4219 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3438 moved from start: 0.8732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 2315 Z= 0.285 Angle : 0.822 9.179 3140 Z= 0.428 Chirality : 0.047 0.237 357 Planarity : 0.006 0.047 371 Dihedral : 5.429 21.893 306 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.66 % Allowed : 20.73 % 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: -0.96 (0.50), residues: 264 helix: 0.40 (0.35), residues: 209 sheet: None (None), residues: 0 loop : -4.70 (0.59), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 455 HIS 0.007 0.002 HIS B 59 PHE 0.009 0.001 PHE B 432 TYR 0.015 0.002 TYR B 468 ARG 0.005 0.001 ARG B 481 *********************** 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 30 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: B 169 MET cc_start: 0.2394 (mmm) cc_final: 0.1822 (mtp) REVERT: B 421 MET cc_start: 0.2293 (tpp) cc_final: 0.1796 (tpp) REVERT: B 481 ARG cc_start: 0.2657 (ttm-80) cc_final: 0.1881 (mtt180) outliers start: 9 outliers final: 4 residues processed: 27 average time/residue: 0.1204 time to fit residues: 4.1378 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 : 0.222 ------------------------------------------------------------------------------- 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 201 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 4 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 19 optimal weight: 0.0670 chunk 15 optimal weight: 0.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.4623 r_free = 0.4623 target = 0.239987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.209255 restraints weight = 2646.216| |-----------------------------------------------------------------------------| r_work (start): 0.4377 rms_B_bonded: 3.43 r_work: 0.4206 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4149 moved from start: 1.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 2315 Z= 0.288 Angle : 0.836 9.342 3140 Z= 0.432 Chirality : 0.047 0.171 357 Planarity : 0.006 0.058 371 Dihedral : 6.289 33.543 306 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.66 % Allowed : 23.98 % 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: -0.83 (0.52), residues: 264 helix: 0.43 (0.36), residues: 210 sheet: None (None), residues: 0 loop : -4.41 (0.63), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 165 HIS 0.005 0.002 HIS B 59 PHE 0.010 0.001 PHE B 432 TYR 0.012 0.002 TYR B 214 ARG 0.004 0.001 ARG B 219 *********************** 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 35 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.229 Fit side-chains REVERT: B 53 ARG cc_start: 0.5430 (tpt170) cc_final: 0.5097 (tpt90) REVERT: B 56 ARG cc_start: 0.4881 (tpt170) cc_final: 0.3739 (mmt90) REVERT: B 97 ARG cc_start: 0.5446 (ttp80) cc_final: 0.5237 (ptm160) REVERT: B 169 MET cc_start: 0.3434 (mmm) cc_final: 0.2846 (mtt) outliers start: 9 outliers final: 6 residues processed: 32 average time/residue: 0.1770 time to fit residues: 6.6640 Evaluate side-chains 32 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 208 TRP Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 450 HIS 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: 0.6980 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4712 r_free = 0.4712 target = 0.245060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.210253 restraints weight = 2553.490| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 3.44 r_work: 0.4180 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4341 moved from start: 1.6591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 2315 Z= 0.348 Angle : 0.957 11.881 3140 Z= 0.499 Chirality : 0.053 0.199 357 Planarity : 0.007 0.067 371 Dihedral : 6.297 24.187 306 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 4.07 % Allowed : 26.83 % Favored : 69.11 % 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: -1.78 (0.48), residues: 264 helix: -0.35 (0.33), residues: 212 sheet: None (None), residues: 0 loop : -4.37 (0.64), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 455 HIS 0.011 0.003 HIS B 59 PHE 0.021 0.002 PHE B 432 TYR 0.020 0.002 TYR B 138 ARG 0.005 0.001 ARG B 143 *********************** 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 41 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.221 Fit side-chains REVERT: B 24 SER cc_start: 0.6772 (m) cc_final: 0.6562 (t) REVERT: B 53 ARG cc_start: 0.5398 (tpt170) cc_final: 0.5081 (tpt90) REVERT: B 56 ARG cc_start: 0.5275 (tpt170) cc_final: 0.4452 (mmt90) REVERT: B 83 MET cc_start: 0.3613 (tmm) cc_final: 0.2924 (ttm) REVERT: B 93 TRP cc_start: 0.6924 (t-100) cc_final: 0.6618 (t-100) REVERT: B 166 ASN cc_start: 0.7458 (t160) cc_final: 0.7146 (m-40) REVERT: B 186 ASP cc_start: 0.8214 (t0) cc_final: 0.7829 (t0) REVERT: B 435 PHE cc_start: 0.4387 (OUTLIER) cc_final: 0.4150 (t80) outliers start: 10 outliers final: 7 residues processed: 39 average time/residue: 0.1521 time to fit residues: 7.0145 Evaluate side-chains 39 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 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 182 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 450 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 17 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4677 r_free = 0.4677 target = 0.240776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.204977 restraints weight = 2627.712| |-----------------------------------------------------------------------------| r_work (start): 0.4315 rms_B_bonded: 3.58 r_work: 0.4166 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4942 moved from start: 1.7221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 2315 Z= 0.283 Angle : 0.740 8.142 3140 Z= 0.386 Chirality : 0.046 0.205 357 Planarity : 0.005 0.050 371 Dihedral : 5.892 27.430 306 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 4.47 % Allowed : 27.64 % Favored : 67.89 % 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: -0.82 (0.50), residues: 264 helix: 0.50 (0.35), residues: 202 sheet: None (None), residues: 0 loop : -4.10 (0.63), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 189 HIS 0.007 0.003 HIS B 59 PHE 0.016 0.002 PHE B 184 TYR 0.010 0.002 TYR B 214 ARG 0.002 0.000 ARG B 481 *********************** 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 38 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.254 Fit side-chains REVERT: B 53 ARG cc_start: 0.5831 (tpt170) cc_final: 0.5564 (tpt90) REVERT: B 56 ARG cc_start: 0.5639 (tpt170) cc_final: 0.4461 (mmt90) REVERT: B 83 MET cc_start: 0.4416 (tmm) cc_final: 0.3634 (mtt) REVERT: B 93 TRP cc_start: 0.7324 (t-100) cc_final: 0.6889 (t-100) REVERT: B 166 ASN cc_start: 0.7696 (t160) cc_final: 0.7398 (m110) outliers start: 11 outliers final: 7 residues processed: 34 average time/residue: 0.1623 time to fit residues: 6.5827 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 : 0.226 ------------------------------------------------------------------------------- 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 196 ILE Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 432 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.0970 chunk 5 optimal weight: 0.0040 chunk 11 optimal weight: 2.9990 overall best weight: 0.3590 ------------------------------------------------------------------------------- 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 = 0.4621 r_free = 0.4621 target = 0.233711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.200905 restraints weight = 2744.241| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 3.58 r_work: 0.4088 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4307 moved from start: 1.8158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2315 Z= 0.223 Angle : 0.702 7.124 3140 Z= 0.361 Chirality : 0.043 0.145 357 Planarity : 0.005 0.053 371 Dihedral : 5.281 22.219 306 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.44 % Allowed : 29.27 % Favored : 68.29 % 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: -0.28 (0.52), residues: 264 helix: 0.96 (0.36), residues: 201 sheet: None (None), residues: 0 loop : -4.10 (0.67), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 189 HIS 0.006 0.002 HIS B 59 PHE 0.015 0.001 PHE B 435 TYR 0.017 0.002 TYR B 431 ARG 0.003 0.001 ARG B 219 *********************** 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: 6 poor density : 26 time to evaluate : 0.237 Fit side-chains REVERT: B 56 ARG cc_start: 0.5013 (tpt170) cc_final: 0.4113 (mmt90) REVERT: B 81 MET cc_start: 0.4392 (ttp) cc_final: 0.3391 (mmt) REVERT: B 83 MET cc_start: 0.4337 (tmm) cc_final: 0.3950 (mtt) REVERT: B 106 MET cc_start: 0.5059 (OUTLIER) cc_final: 0.4642 (tpp) REVERT: B 139 ARG cc_start: 0.6992 (tmm-80) cc_final: 0.6778 (tmm-80) REVERT: B 166 ASN cc_start: 0.7384 (t160) cc_final: 0.7182 (m-40) outliers start: 6 outliers final: 3 residues processed: 29 average time/residue: 0.2216 time to fit residues: 7.4002 Evaluate side-chains 28 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 416 GLN 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: 0.0970 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 13 optimal weight: 0.0770 chunk 0 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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 = 0.4577 r_free = 0.4577 target = 0.228291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.194016 restraints weight = 2613.809| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 3.43 r_work: 0.4023 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4435 moved from start: 1.9009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2315 Z= 0.240 Angle : 0.726 8.204 3140 Z= 0.375 Chirality : 0.044 0.147 357 Planarity : 0.005 0.059 371 Dihedral : 5.455 21.994 306 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 2.03 % Allowed : 30.49 % Favored : 67.48 % 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: -0.47 (0.50), residues: 264 helix: 0.74 (0.35), residues: 203 sheet: None (None), residues: 0 loop : -3.99 (0.66), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 428 HIS 0.008 0.002 HIS B 59 PHE 0.018 0.002 PHE B 435 TYR 0.016 0.002 TYR B 431 ARG 0.008 0.001 ARG B 53 *********************** 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 33 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.271 Fit side-chains REVERT: B 56 ARG cc_start: 0.4933 (tpt170) cc_final: 0.4361 (mmt90) REVERT: B 170 GLN cc_start: 0.5211 (OUTLIER) cc_final: 0.4906 (mp10) outliers start: 5 outliers final: 4 residues processed: 31 average time/residue: 0.1838 time to fit residues: 6.8362 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 : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 429 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 0.0670 chunk 15 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.227526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.191947 restraints weight = 2617.280| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 3.44 r_work: 0.4034 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4552 moved from start: 1.9734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2315 Z= 0.257 Angle : 0.729 7.115 3140 Z= 0.377 Chirality : 0.046 0.240 357 Planarity : 0.005 0.058 371 Dihedral : 5.426 21.439 306 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.03 % Allowed : 31.71 % Favored : 66.26 % 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: -0.39 (0.51), residues: 264 helix: 0.78 (0.35), residues: 204 sheet: None (None), residues: 0 loop : -3.94 (0.69), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 189 HIS 0.009 0.003 HIS B 59 PHE 0.014 0.002 PHE B 432 TYR 0.011 0.002 TYR B 138 ARG 0.009 0.001 ARG B 139 ********************** 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 32 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.251 Fit side-chains REVERT: B 56 ARG cc_start: 0.4952 (tpt170) cc_final: 0.4300 (mmt90) REVERT: B 81 MET cc_start: 0.3990 (ttp) cc_final: 0.3654 (mtp) outliers start: 5 outliers final: 4 residues processed: 30 average time/residue: 0.1612 time to fit residues: 6.0223 Evaluate side-chains 30 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 429 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 0.0870 chunk 19 optimal weight: 0.0870 chunk 4 optimal weight: 0.7980 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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 = 0.4571 r_free = 0.4571 target = 0.228184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.193320 restraints weight = 2582.055| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 3.40 r_work: 0.3991 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4539 moved from start: 2.0301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2315 Z= 0.228 Angle : 0.697 7.442 3140 Z= 0.357 Chirality : 0.045 0.193 357 Planarity : 0.005 0.053 371 Dihedral : 5.159 21.633 306 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.03 % Allowed : 31.30 % Favored : 66.67 % 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: -0.28 (0.51), residues: 264 helix: 0.87 (0.35), residues: 204 sheet: None (None), residues: 0 loop : -4.00 (0.67), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 189 HIS 0.007 0.001 HIS B 59 PHE 0.012 0.001 PHE B 435 TYR 0.011 0.001 TYR B 431 ARG 0.003 0.000 ARG B 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1632.20 seconds wall clock time: 30 minutes 4.04 seconds (1804.04 seconds total)