Starting phenix.real_space_refine on Mon Jun 24 13:27:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x63_38078/06_2024/8x63_38078_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x63_38078/06_2024/8x63_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x63_38078/06_2024/8x63_38078.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x63_38078/06_2024/8x63_38078.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x63_38078/06_2024/8x63_38078_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x63_38078/06_2024/8x63_38078_updated.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 2.31, per 1000 atoms: 1.03 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 378.8 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... running ksdssp... Secondary structure from input PDB file: 11 helices and 0 sheets defined 79.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'B' and resid 28 through 54 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 61 through 89 Proline residue: B 82 - end of helix Processing helix chain 'B' and resid 97 through 128 removed outlier: 4.443A pdb=" N PHE B 119 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 163 Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 183 through 186 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 183 through 186' Processing helix chain 'B' and resid 188 through 220 Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 409 through 426 Processing helix chain 'B' and resid 429 through 440 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 444 No H-bonds generated for 'chain 'B' and resid 442 through 444' Processing helix chain 'B' and resid 447 through 471 Proline residue: B 465 - end of helix Proline residue: B 469 - end of helix Processing helix chain 'B' and resid 473 through 480 removed outlier: 3.727A pdb=" N LYS B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) 150 hydrogen bonds defined for protein. 450 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: 0.62 Time building geometry restraints manager: 0.87 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: 98.07 - 105.26: 40 105.26 - 112.45: 1186 112.45 - 119.64: 779 119.64 - 126.83: 1092 126.83 - 134.03: 43 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: 882 2.91 - 3.41: 2396 3.41 - 3.90: 3524 3.90 - 4.40: 3904 4.40 - 4.90: 6394 Nonbonded interactions: 17100 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 2.520 nonbonded pdb=" O HIS B 450 " pdb=" OG1 THR B 453 " model vdw 2.516 2.440 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 17095 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: 0.810 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: 3.460 Check model and map are aligned: 0.010 Set scattering table: 0.040 Process input model: 12.110 Find NCS groups from input model: 0.070 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.570 ------------------------------------------------------------------------------- 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= 0.389 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 fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.220 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: 0.1400 time to fit residues: 4.6722 Evaluate side-chains 18 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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: 0.6980 chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 0.0370 chunk 10 optimal weight: 0.0470 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2418 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 2315 Z= 0.335 Angle : 0.865 8.618 3140 Z= 0.434 Chirality : 0.047 0.135 357 Planarity : 0.007 0.058 371 Dihedral : 5.472 25.166 308 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.41 % Allowed : 10.57 % Favored : 89.02 % 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: -0.11 (0.51), residues: 264 helix: 1.02 (0.35), residues: 206 sheet: None (None), residues: 0 loop : -4.18 (0.60), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.005 TRP B 93 HIS 0.003 0.001 HIS B 167 PHE 0.019 0.002 PHE B 432 TYR 0.010 0.002 TYR B 87 ARG 0.004 0.001 ARG B 53 *********************** 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 21 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.229 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 20 average time/residue: 0.1372 time to fit residues: 3.4602 Evaluate side-chains 16 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.174 ------------------------------------------------------------------------------- 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 13 optimal weight: 0.2980 chunk 7 optimal weight: 0.0870 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 0.0870 chunk 18 optimal weight: 0.4980 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3174 moved from start: 0.6093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 2315 Z= 0.266 Angle : 0.761 9.321 3140 Z= 0.383 Chirality : 0.043 0.126 357 Planarity : 0.006 0.057 371 Dihedral : 6.379 34.346 306 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.03 % Allowed : 14.23 % Favored : 83.74 % 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: -0.40 (0.51), residues: 264 helix: 0.89 (0.35), residues: 207 sheet: None (None), residues: 0 loop : -4.72 (0.58), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 93 HIS 0.005 0.001 HIS B 59 PHE 0.011 0.001 PHE B 424 TYR 0.013 0.002 TYR B 468 ARG 0.005 0.001 ARG B 481 *********************** 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 26 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.235 Fit side-chains REVERT: B 169 MET cc_start: 0.0683 (mmm) cc_final: -0.0239 (mtp) REVERT: B 451 MET cc_start: 0.4054 (ptp) cc_final: 0.2152 (mmp) outliers start: 5 outliers final: 3 residues processed: 22 average time/residue: 0.1390 time to fit residues: 3.9001 Evaluate side-chains 20 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 17 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.0570 chunk 16 optimal weight: 0.1980 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.0570 chunk 23 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4175 moved from start: 0.9329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 2315 Z= 0.307 Angle : 0.780 8.379 3140 Z= 0.407 Chirality : 0.048 0.189 357 Planarity : 0.006 0.050 371 Dihedral : 5.540 19.867 306 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.47 % Allowed : 17.89 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.51), residues: 264 helix: 0.54 (0.36), residues: 205 sheet: None (None), residues: 0 loop : -4.55 (0.55), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 93 HIS 0.006 0.001 HIS B 59 PHE 0.008 0.001 PHE B 475 TYR 0.011 0.002 TYR B 468 ARG 0.006 0.001 ARG B 219 *********************** 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 36 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 25 time to evaluate : 0.287 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 33 average time/residue: 0.1113 time to fit residues: 4.6852 Evaluate side-chains 25 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 20 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 203 THR Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 429 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 0.3980 chunk 10 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4599 moved from start: 1.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2315 Z= 0.267 Angle : 0.764 10.046 3140 Z= 0.388 Chirality : 0.044 0.134 357 Planarity : 0.006 0.058 371 Dihedral : 6.293 29.178 306 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.47 % Allowed : 21.95 % Favored : 73.58 % 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: -0.59 (0.50), residues: 264 helix: 0.70 (0.36), residues: 201 sheet: None (None), residues: 0 loop : -4.07 (0.59), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 428 HIS 0.008 0.002 HIS B 59 PHE 0.014 0.001 PHE B 432 TYR 0.014 0.002 TYR B 214 ARG 0.002 0.000 ARG B 411 *********************** 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 37 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 26 time to evaluate : 0.228 Fit side-chains REVERT: B 56 ARG cc_start: 0.5063 (tpt170) cc_final: 0.3822 (mmt90) outliers start: 11 outliers final: 7 residues processed: 34 average time/residue: 0.1597 time to fit residues: 6.4426 Evaluate side-chains 32 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 25 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 203 THR Chi-restraints excluded: chain B residue 416 GLN 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 6 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 0.0770 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 0.0470 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 19 optimal weight: 0.0270 chunk 16 optimal weight: 0.6980 overall best weight: 0.3294 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4867 moved from start: 1.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2315 Z= 0.233 Angle : 0.719 6.591 3140 Z= 0.366 Chirality : 0.044 0.141 357 Planarity : 0.005 0.044 371 Dihedral : 5.609 20.998 306 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % 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: -0.50 (0.49), residues: 264 helix: 0.74 (0.35), residues: 203 sheet: None (None), residues: 0 loop : -4.10 (0.58), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 93 HIS 0.007 0.002 HIS B 59 PHE 0.015 0.001 PHE B 199 TYR 0.016 0.002 TYR B 468 ARG 0.003 0.001 ARG B 97 *********************** 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 34 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 25 time to evaluate : 0.213 Fit side-chains REVERT: B 56 ARG cc_start: 0.5553 (tpt170) cc_final: 0.3998 (mmt90) REVERT: B 421 MET cc_start: 0.4997 (tpp) cc_final: 0.4723 (mmp) outliers start: 9 outliers final: 5 residues processed: 33 average time/residue: 0.1297 time to fit residues: 5.2281 Evaluate side-chains 30 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 416 GLN 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 15 optimal weight: 5.9990 chunk 12 optimal weight: 0.0970 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.0020 chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.0170 chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.2824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4988 moved from start: 1.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2315 Z= 0.195 Angle : 0.679 7.722 3140 Z= 0.343 Chirality : 0.042 0.162 357 Planarity : 0.005 0.041 371 Dihedral : 5.484 22.338 306 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.66 % Allowed : 25.61 % 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: -0.50 (0.50), residues: 264 helix: 0.74 (0.35), residues: 205 sheet: None (None), residues: 0 loop : -4.24 (0.58), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 93 HIS 0.005 0.002 HIS B 59 PHE 0.010 0.001 PHE B 432 TYR 0.013 0.001 TYR B 468 ARG 0.002 0.000 ARG B 411 *********************** 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 34 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 25 time to evaluate : 0.217 Fit side-chains REVERT: B 56 ARG cc_start: 0.5597 (tpt170) cc_final: 0.4057 (mmt90) REVERT: B 83 MET cc_start: 0.3016 (tmm) cc_final: 0.2097 (ttm) REVERT: B 436 MET cc_start: 0.6779 (tpp) cc_final: 0.6385 (tpp) outliers start: 9 outliers final: 8 residues processed: 33 average time/residue: 0.1380 time to fit residues: 5.6131 Evaluate side-chains 32 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 24 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 203 THR Chi-restraints excluded: chain B residue 221 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.0970 chunk 24 optimal weight: 0.6980 chunk 14 optimal weight: 0.0470 chunk 10 optimal weight: 0.0870 chunk 19 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 0.0010 chunk 25 optimal weight: 0.0980 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 overall best weight: 0.0660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4904 moved from start: 1.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2315 Z= 0.176 Angle : 0.662 8.836 3140 Z= 0.330 Chirality : 0.039 0.157 357 Planarity : 0.004 0.035 371 Dihedral : 5.234 22.921 306 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.85 % Allowed : 26.02 % 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: -0.25 (0.51), residues: 264 helix: 0.96 (0.35), residues: 206 sheet: None (None), residues: 0 loop : -4.43 (0.54), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 93 HIS 0.006 0.002 HIS B 450 PHE 0.011 0.001 PHE B 432 TYR 0.009 0.001 TYR B 468 ARG 0.002 0.000 ARG B 125 *********************** 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 34 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 27 time to evaluate : 0.237 Fit side-chains REVERT: B 56 ARG cc_start: 0.5555 (tpt170) cc_final: 0.4174 (mmt90) REVERT: B 83 MET cc_start: 0.2800 (tmm) cc_final: 0.2059 (ttm) REVERT: B 436 MET cc_start: 0.6711 (tpp) cc_final: 0.6386 (tpp) outliers start: 7 outliers final: 6 residues processed: 32 average time/residue: 0.1389 time to fit residues: 5.4446 Evaluate side-chains 33 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 27 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 201 LEU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 221 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 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 3 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5424 moved from start: 1.5986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 2315 Z= 0.300 Angle : 0.825 13.542 3140 Z= 0.423 Chirality : 0.048 0.196 357 Planarity : 0.005 0.040 371 Dihedral : 5.889 22.125 306 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 4.07 % Allowed : 23.58 % 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: -0.91 (0.49), residues: 264 helix: 0.40 (0.34), residues: 209 sheet: None (None), residues: 0 loop : -4.49 (0.58), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 165 HIS 0.008 0.002 HIS B 59 PHE 0.014 0.002 PHE B 199 TYR 0.015 0.002 TYR B 468 ARG 0.004 0.001 ARG B 411 *********************** 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 fitting. rotamer outliers: 10 poor density : 24 time to evaluate : 0.224 Fit side-chains REVERT: B 56 ARG cc_start: 0.6176 (tpt170) cc_final: 0.4895 (mmt90) REVERT: B 221 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.5788 (pt) REVERT: B 451 MET cc_start: 0.4690 (OUTLIER) cc_final: 0.4451 (mmm) outliers start: 10 outliers final: 7 residues processed: 32 average time/residue: 0.1114 time to fit residues: 4.3744 Evaluate side-chains 33 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 24 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 109 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 451 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 0.2980 chunk 21 optimal weight: 0.2980 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 0.2980 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5446 moved from start: 1.6841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2315 Z= 0.234 Angle : 0.697 8.633 3140 Z= 0.353 Chirality : 0.041 0.137 357 Planarity : 0.005 0.043 371 Dihedral : 5.465 22.301 306 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.85 % Allowed : 23.98 % Favored : 73.17 % 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: -0.59 (0.50), residues: 264 helix: 0.60 (0.35), residues: 209 sheet: None (None), residues: 0 loop : -4.30 (0.59), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 93 HIS 0.006 0.001 HIS B 59 PHE 0.011 0.001 PHE B 432 TYR 0.016 0.002 TYR B 468 ARG 0.002 0.000 ARG B 481 ********************** 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 fitting. rotamer outliers: 7 poor density : 25 time to evaluate : 0.188 Fit side-chains REVERT: B 56 ARG cc_start: 0.5908 (tpt170) cc_final: 0.4372 (mmt180) REVERT: B 206 MET cc_start: 0.5888 (tmm) cc_final: 0.5677 (tmm) REVERT: B 221 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.5766 (pt) outliers start: 7 outliers final: 6 residues processed: 31 average time/residue: 0.1291 time to fit residues: 4.8701 Evaluate side-chains 30 residues out of total 246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 23 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 420 ILE 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 18 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.0770 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.0570 overall best weight: 0.3856 ------------------------------------------------------------------------------- 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 = 0.4666 r_free = 0.4666 target = 0.240277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.205493 restraints weight = 2626.947| |-----------------------------------------------------------------------------| r_work (start): 0.4316 rms_B_bonded: 3.58 r_work: 0.4168 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4320 moved from start: 1.7428 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= 0.223 Angle : 0.698 6.383 3140 Z= 0.361 Chirality : 0.042 0.143 357 Planarity : 0.005 0.041 371 Dihedral : 6.397 36.952 306 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 3.25 % Allowed : 23.98 % Favored : 72.76 % 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: -0.44 (0.50), residues: 264 helix: 0.72 (0.34), residues: 209 sheet: None (None), residues: 0 loop : -4.31 (0.61), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 93 HIS 0.007 0.001 HIS B 59 PHE 0.010 0.001 PHE B 432 TYR 0.019 0.002 TYR B 468 ARG 0.001 0.000 ARG B 411 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1115.61 seconds wall clock time: 20 minutes 59.03 seconds (1259.03 seconds total)