Starting phenix.real_space_refine on Fri Apr 5 12:30:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jv2_22491/04_2024/7jv2_22491.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jv2_22491/04_2024/7jv2_22491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jv2_22491/04_2024/7jv2_22491.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jv2_22491/04_2024/7jv2_22491.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jv2_22491/04_2024/7jv2_22491.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jv2_22491/04_2024/7jv2_22491.pdb" } resolution = 3.5 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= 0.023 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 8 5.16 5 C 1361 2.51 5 N 363 2.21 5 O 419 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 6": "OE1" <-> "OE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 73": "OD1" <-> "OD2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 90": "OD1" <-> "OD2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 52": "OD1" <-> "OD2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 84": "OD1" <-> "OD2" Residue "L TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 2151 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 915 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 812 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "A" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain breaks: 1 Time building chain proxies: 1.72, per 1000 atoms: 0.80 Number of scatterers: 2151 At special positions: 0 Unit cell: (68.25, 55.65, 66.15, 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 8 16.00 O 419 8.00 N 363 7.00 C 1361 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.01 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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: 0.77 Conformation dependent library (CDL) restraints added in 377.9 milliseconds 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 494 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 8 sheets defined 5.0% alpha, 40.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'L' and resid 30 through 34 Processing helix chain 'L' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 5.839A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.513A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 90 hydrogen bonds defined for protein. 195 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: 0.55 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 459 1.32 - 1.45: 593 1.45 - 1.57: 1134 1.57 - 1.69: 8 1.69 - 1.82: 10 Bond restraints: 2204 Sorted by residual: bond pdb=" CB ILE A 468 " pdb=" CG1 ILE A 468 " ideal model delta sigma weight residual 1.530 1.623 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" CB LEU A 461 " pdb=" CG LEU A 461 " ideal model delta sigma weight residual 1.530 1.610 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" CB LEU L 110 " pdb=" CG LEU L 110 " ideal model delta sigma weight residual 1.530 1.597 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" CB ILE H 70 " pdb=" CG1 ILE H 70 " ideal model delta sigma weight residual 1.530 1.468 0.062 2.00e-02 2.50e+03 9.52e+00 bond pdb=" CG GLN L 1 " pdb=" CD GLN L 1 " ideal model delta sigma weight residual 1.516 1.587 -0.071 2.50e-02 1.60e+03 8.01e+00 ... (remaining 2199 not shown) Histogram of bond angle deviations from ideal: 100.81 - 107.41: 86 107.41 - 114.01: 1118 114.01 - 120.62: 963 120.62 - 127.22: 805 127.22 - 133.82: 19 Bond angle restraints: 2991 Sorted by residual: angle pdb=" C GLN A 498 " pdb=" N PRO A 499 " pdb=" CA PRO A 499 " ideal model delta sigma weight residual 119.82 126.78 -6.96 9.80e-01 1.04e+00 5.04e+01 angle pdb=" C PHE A 490 " pdb=" N PRO A 491 " pdb=" CA PRO A 491 " ideal model delta sigma weight residual 119.56 125.42 -5.86 1.01e+00 9.80e-01 3.36e+01 angle pdb=" C GLU L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta sigma weight residual 119.32 125.73 -6.41 1.14e+00 7.69e-01 3.16e+01 angle pdb=" C ALA L 45 " pdb=" N PRO L 46 " pdb=" CA PRO L 46 " ideal model delta sigma weight residual 119.76 125.21 -5.45 1.00e+00 1.00e+00 2.97e+01 angle pdb=" C ARG L 81 " pdb=" N PRO L 82 " pdb=" CA PRO L 82 " ideal model delta sigma weight residual 119.47 125.67 -6.20 1.16e+00 7.43e-01 2.86e+01 ... (remaining 2986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 1219 17.29 - 34.57: 35 34.57 - 51.85: 10 51.85 - 69.14: 3 69.14 - 86.42: 5 Dihedral angle restraints: 1272 sinusoidal: 479 harmonic: 793 Sorted by residual: dihedral pdb=" CB GLU H 46 " pdb=" CG GLU H 46 " pdb=" CD GLU H 46 " pdb=" OE1 GLU H 46 " ideal model delta sinusoidal sigma weight residual 0.00 -86.42 86.42 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" N TYR H 59 " pdb=" CA TYR H 59 " pdb=" CB TYR H 59 " pdb=" CG TYR H 59 " ideal model delta sinusoidal sigma weight residual -180.00 -123.33 -56.67 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" CB GLU H 6 " pdb=" CG GLU H 6 " pdb=" CD GLU H 6 " pdb=" OE1 GLU H 6 " ideal model delta sinusoidal sigma weight residual 0.00 -82.50 82.50 1 3.00e+01 1.11e-03 9.27e+00 ... (remaining 1269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 216 0.069 - 0.139: 85 0.139 - 0.208: 11 0.208 - 0.277: 2 0.277 - 0.347: 2 Chirality restraints: 316 Sorted by residual: chirality pdb=" CG LEU L 110 " pdb=" CB LEU L 110 " pdb=" CD1 LEU L 110 " pdb=" CD2 LEU L 110 " both_signs ideal model delta sigma weight residual False -2.59 -2.94 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CG LEU A 461 " pdb=" CB LEU A 461 " pdb=" CD1 LEU A 461 " pdb=" CD2 LEU A 461 " both_signs ideal model delta sigma weight residual False -2.59 -2.93 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CB ILE A 468 " pdb=" CA ILE A 468 " pdb=" CG1 ILE A 468 " pdb=" CG2 ILE A 468 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 313 not shown) Planarity restraints: 385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 32 " -0.042 2.00e-02 2.50e+03 2.24e-02 1.00e+01 pdb=" CG TYR H 32 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR H 32 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR H 32 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR H 32 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR H 32 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR H 32 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 32 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 105 " 0.036 2.00e-02 2.50e+03 1.86e-02 6.94e+00 pdb=" CG TYR H 105 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR H 105 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR H 105 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR H 105 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR H 105 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR H 105 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 105 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 33 " 0.030 2.00e-02 2.50e+03 1.50e-02 5.63e+00 pdb=" CG TRP H 33 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP H 33 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP H 33 " -0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP H 33 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP H 33 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP H 33 " -0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 33 " 0.016 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 33 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP H 33 " 0.015 2.00e-02 2.50e+03 ... (remaining 382 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 1312 3.05 - 3.51: 1905 3.51 - 3.97: 3466 3.97 - 4.44: 3915 4.44 - 4.90: 6436 Nonbonded interactions: 17034 Sorted by model distance: nonbonded pdb=" N HIS L 33 " pdb=" N TYR L 34 " model vdw 2.587 2.560 nonbonded pdb=" N LYS H 76 " pdb=" N ASN H 77 " model vdw 2.587 2.560 nonbonded pdb=" N SER H 71 " pdb=" O SER H 71 " model vdw 2.589 2.496 nonbonded pdb=" N ASP H 62 " pdb=" OD1 ASP H 62 " model vdw 2.594 2.520 nonbonded pdb=" O TYR L 34 " pdb=" CB TYR L 34 " model vdw 2.596 2.752 ... (remaining 17029 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.430 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.780 Find NCS groups from input model: 0.060 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 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 : 0.015 0.093 2204 Z= 0.946 Angle : 1.386 6.959 2991 Z= 0.934 Chirality : 0.075 0.347 316 Planarity : 0.006 0.022 385 Dihedral : 11.432 86.421 769 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.32 % Allowed : 0.88 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.50), residues: 274 helix: None (None), residues: 0 sheet: 0.23 (0.50), residues: 102 loop : 0.93 (0.47), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.006 TRP H 33 HIS 0.002 0.001 HIS L 57 PHE 0.018 0.004 PHE L 101 TYR 0.042 0.007 TYR H 32 ARG 0.003 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.230 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 65 average time/residue: 0.1529 time to fit residues: 11.4102 Evaluate side-chains 45 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 0.0870 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.0980 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 0.0970 chunk 21 optimal weight: 0.0970 chunk 8 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 overall best weight: 0.1554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN L 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2204 Z= 0.186 Angle : 0.612 7.607 2991 Z= 0.325 Chirality : 0.043 0.148 316 Planarity : 0.003 0.022 385 Dihedral : 4.552 15.634 310 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.20 % Allowed : 10.13 % Favored : 87.67 % 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: 0.51 (0.48), residues: 274 helix: None (None), residues: 0 sheet: 0.23 (0.46), residues: 112 loop : 0.58 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 33 HIS 0.002 0.001 HIS L 57 PHE 0.009 0.001 PHE L 101 TYR 0.011 0.001 TYR H 80 ARG 0.002 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: L 31 SER cc_start: 0.7706 (m) cc_final: 0.7210 (t) REVERT: L 47 ARG cc_start: 0.8599 (ptm160) cc_final: 0.8347 (ptm160) REVERT: L 87 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7880 (mm-30) outliers start: 5 outliers final: 3 residues processed: 56 average time/residue: 0.1171 time to fit residues: 7.8044 Evaluate side-chains 50 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 10 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 18 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: H 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 2204 Z= 0.341 Angle : 0.683 7.421 2991 Z= 0.362 Chirality : 0.044 0.150 316 Planarity : 0.003 0.025 385 Dihedral : 5.065 17.250 310 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.96 % Allowed : 9.69 % Favored : 86.34 % 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: 0.21 (0.48), residues: 274 helix: None (None), residues: 0 sheet: 0.37 (0.46), residues: 115 loop : 0.06 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 33 HIS 0.002 0.001 HIS L 57 PHE 0.013 0.002 PHE L 101 TYR 0.021 0.002 TYR H 60 ARG 0.002 0.001 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: L 31 SER cc_start: 0.7760 (m) cc_final: 0.7335 (t) REVERT: L 87 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7958 (mm-30) outliers start: 9 outliers final: 8 residues processed: 52 average time/residue: 0.1160 time to fit residues: 7.3156 Evaluate side-chains 50 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 455 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.0970 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 23 optimal weight: 0.0870 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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: 0.7540 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 2204 Z= 0.345 Angle : 0.684 7.239 2991 Z= 0.363 Chirality : 0.044 0.138 316 Planarity : 0.004 0.024 385 Dihedral : 5.197 18.123 310 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 6.61 % Allowed : 11.01 % Favored : 82.38 % 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: -0.22 (0.48), residues: 274 helix: None (None), residues: 0 sheet: 0.10 (0.46), residues: 115 loop : -0.26 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 33 HIS 0.002 0.001 HIS L 57 PHE 0.016 0.002 PHE L 101 TYR 0.019 0.002 TYR H 60 ARG 0.002 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 45 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: L 87 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7956 (mm-30) outliers start: 15 outliers final: 13 residues processed: 51 average time/residue: 0.0960 time to fit residues: 6.1919 Evaluate side-chains 57 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 44 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 495 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 6 optimal weight: 0.0670 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 0.1980 chunk 15 optimal weight: 0.0170 overall best weight: 0.2956 ------------------------------------------------------------------------------- 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: 0.7512 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 2204 Z= 0.259 Angle : 0.628 6.938 2991 Z= 0.331 Chirality : 0.042 0.131 316 Planarity : 0.003 0.027 385 Dihedral : 4.927 18.691 310 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 7.05 % Allowed : 12.33 % Favored : 80.62 % 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 (0.48), residues: 274 helix: None (None), residues: 0 sheet: -0.09 (0.47), residues: 112 loop : -0.44 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 33 HIS 0.002 0.001 HIS L 57 PHE 0.020 0.002 PHE L 101 TYR 0.014 0.001 TYR H 60 ARG 0.002 0.000 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 47 time to evaluate : 0.245 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 54 average time/residue: 0.1186 time to fit residues: 8.0260 Evaluate side-chains 59 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 46 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR 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: 0.3980 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 14 optimal weight: 0.0970 chunk 19 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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: 0.7553 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 2204 Z= 0.317 Angle : 0.660 6.885 2991 Z= 0.346 Chirality : 0.044 0.141 316 Planarity : 0.004 0.031 385 Dihedral : 5.076 18.992 310 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 7.05 % Allowed : 13.66 % Favored : 79.30 % 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: -0.86 (0.47), residues: 274 helix: None (None), residues: 0 sheet: -0.35 (0.47), residues: 107 loop : -0.67 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 33 HIS 0.003 0.002 HIS L 57 PHE 0.017 0.002 PHE L 101 TYR 0.017 0.002 TYR H 60 ARG 0.004 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 51 time to evaluate : 0.267 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 14 residues processed: 57 average time/residue: 0.1035 time to fit residues: 7.3090 Evaluate side-chains 63 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 49 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 0.1980 chunk 17 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 23 optimal weight: 0.4980 chunk 24 optimal weight: 0.0980 overall best weight: 0.2380 ------------------------------------------------------------------------------- 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: 0.7502 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 2204 Z= 0.219 Angle : 0.601 6.731 2991 Z= 0.315 Chirality : 0.042 0.127 316 Planarity : 0.004 0.033 385 Dihedral : 4.801 18.887 310 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 7.49 % Allowed : 13.66 % Favored : 78.85 % 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 (0.47), residues: 274 helix: None (None), residues: 0 sheet: -0.51 (0.46), residues: 107 loop : -0.67 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 33 HIS 0.002 0.001 HIS L 57 PHE 0.014 0.002 PHE L 101 TYR 0.012 0.001 TYR H 60 ARG 0.003 0.000 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 50 time to evaluate : 0.280 Fit side-chains outliers start: 17 outliers final: 14 residues processed: 57 average time/residue: 0.1156 time to fit residues: 8.3577 Evaluate side-chains 60 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 46 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 0.0670 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.0970 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 overall best weight: 0.4116 ------------------------------------------------------------------------------- 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: 0.7574 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 2204 Z= 0.341 Angle : 0.683 7.102 2991 Z= 0.356 Chirality : 0.045 0.155 316 Planarity : 0.004 0.033 385 Dihedral : 5.158 19.174 310 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 7.93 % Allowed : 14.10 % Favored : 77.97 % 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: -1.24 (0.47), residues: 274 helix: None (None), residues: 0 sheet: -0.77 (0.46), residues: 107 loop : -0.81 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP H 33 HIS 0.003 0.001 HIS L 57 PHE 0.015 0.002 PHE L 101 TYR 0.016 0.002 TYR H 60 ARG 0.004 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 48 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: H 32 TYR cc_start: 0.7282 (m-80) cc_final: 0.7053 (m-80) REVERT: L 72 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6866 (ptmt) outliers start: 18 outliers final: 15 residues processed: 56 average time/residue: 0.0921 time to fit residues: 6.5077 Evaluate side-chains 62 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 46 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 72 LYS Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 chunk 13 optimal weight: 0.0470 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 6 optimal weight: 0.3980 chunk 19 optimal weight: 0.3980 chunk 3 optimal weight: 0.3980 overall best weight: 0.2478 ------------------------------------------------------------------------------- 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: 0.7513 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 2204 Z= 0.228 Angle : 0.613 8.148 2991 Z= 0.317 Chirality : 0.042 0.127 316 Planarity : 0.004 0.035 385 Dihedral : 4.898 19.222 310 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 7.49 % Allowed : 14.54 % Favored : 77.97 % 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: -1.16 (0.48), residues: 274 helix: None (None), residues: 0 sheet: -0.78 (0.46), residues: 107 loop : -0.71 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.001 0.001 HIS L 57 PHE 0.013 0.002 PHE L 101 TYR 0.011 0.001 TYR H 60 ARG 0.003 0.000 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 46 time to evaluate : 0.239 Fit side-chains outliers start: 17 outliers final: 14 residues processed: 54 average time/residue: 0.0875 time to fit residues: 6.0583 Evaluate side-chains 57 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 43 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 0.0060 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 overall best weight: 0.3596 ------------------------------------------------------------------------------- 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: 0.7555 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 2204 Z= 0.304 Angle : 0.678 8.026 2991 Z= 0.349 Chirality : 0.044 0.161 316 Planarity : 0.004 0.035 385 Dihedral : 5.115 18.842 310 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 5.73 % Allowed : 15.86 % Favored : 78.41 % 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: -1.25 (0.48), residues: 274 helix: None (None), residues: 0 sheet: -0.88 (0.47), residues: 107 loop : -0.74 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 33 HIS 0.002 0.001 HIS L 57 PHE 0.014 0.002 PHE L 101 TYR 0.018 0.002 TYR H 60 ARG 0.004 0.000 ARG H 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 45 time to evaluate : 0.235 Fit side-chains outliers start: 13 outliers final: 13 residues processed: 51 average time/residue: 0.0771 time to fit residues: 5.1922 Evaluate side-chains 57 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 44 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.0770 chunk 15 optimal weight: 0.0980 chunk 10 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 3 optimal weight: 0.1980 overall best weight: 0.2338 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.151555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.139682 restraints weight = 3169.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.142191 restraints weight = 1882.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.143843 restraints weight = 1260.812| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2204 Z= 0.221 Angle : 0.647 8.138 2991 Z= 0.326 Chirality : 0.042 0.126 316 Planarity : 0.004 0.036 385 Dihedral : 4.850 18.884 310 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 6.61 % Allowed : 15.86 % Favored : 77.53 % 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: -1.13 (0.48), residues: 274 helix: None (None), residues: 0 sheet: -0.79 (0.48), residues: 105 loop : -0.66 (0.46), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.001 0.001 HIS L 57 PHE 0.013 0.002 PHE L 101 TYR 0.014 0.001 TYR H 60 ARG 0.003 0.000 ARG H 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1154.44 seconds wall clock time: 21 minutes 11.31 seconds (1271.31 seconds total)