Starting phenix.real_space_refine on Sun Mar 10 15:06:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v48_31703/03_2024/7v48_31703.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v48_31703/03_2024/7v48_31703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v48_31703/03_2024/7v48_31703.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v48_31703/03_2024/7v48_31703.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v48_31703/03_2024/7v48_31703.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v48_31703/03_2024/7v48_31703.pdb" } resolution = 3.0 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= 0.006 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: 3 Type Number sf(0) Gaussians C 1626 2.51 5 N 450 2.21 5 O 522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 98": "OD1" <-> "OD2" Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 98": "OD1" <-> "OD2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "F TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 98": "OD1" <-> "OD2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 98": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2598 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "A" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "E" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "C" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "F" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "D" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Time building chain proxies: 1.82, per 1000 atoms: 0.70 Number of scatterers: 2598 At special positions: 0 Unit cell: (104.94, 110.24, 32.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 522 8.00 N 450 7.00 C 1626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.97 Conformation dependent library (CDL) restraints added in 524.1 milliseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 636 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 38 through 40 removed outlier: 6.719A pdb=" N TYR B 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 48 through 50 removed outlier: 6.501A pdb=" N VAL B 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'E' and resid 75 through 79 removed outlier: 6.608A pdb=" N ALA B 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N GLN F 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA B 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 82 through 83 removed outlier: 6.541A pdb=" N VAL B 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 38 through 40 removed outlier: 6.748A pdb=" N TYR A 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 48 through 50 removed outlier: 6.513A pdb=" N VAL A 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 75 through 79 removed outlier: 6.603A pdb=" N ALA A 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N GLN D 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA A 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 82 through 83 removed outlier: 6.549A pdb=" N VAL A 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) 19 hydrogen bonds defined for protein. 57 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: 0.48 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 456 1.29 - 1.36: 408 1.36 - 1.42: 102 1.42 - 1.49: 426 1.49 - 1.55: 1218 Bond restraints: 2610 Sorted by residual: bond pdb=" CA ALA D 90 " pdb=" C ALA D 90 " ideal model delta sigma weight residual 1.530 1.522 0.008 1.10e-02 8.26e+03 4.74e-01 bond pdb=" CA ALA F 90 " pdb=" C ALA F 90 " ideal model delta sigma weight residual 1.530 1.522 0.008 1.10e-02 8.26e+03 4.74e-01 bond pdb=" CA ALA A 90 " pdb=" C ALA A 90 " ideal model delta sigma weight residual 1.530 1.522 0.008 1.10e-02 8.26e+03 4.70e-01 bond pdb=" CA ALA B 90 " pdb=" C ALA B 90 " ideal model delta sigma weight residual 1.530 1.523 0.007 1.10e-02 8.26e+03 4.14e-01 bond pdb=" CA ALA E 90 " pdb=" C ALA E 90 " ideal model delta sigma weight residual 1.530 1.523 0.007 1.10e-02 8.26e+03 4.09e-01 ... (remaining 2605 not shown) Histogram of bond angle deviations from ideal: 105.88 - 110.97: 1036 110.97 - 116.06: 862 116.06 - 121.15: 767 121.15 - 126.24: 857 126.24 - 131.32: 6 Bond angle restraints: 3528 Sorted by residual: angle pdb=" CA ALA F 90 " pdb=" C ALA F 90 " pdb=" N ALA F 91 " ideal model delta sigma weight residual 114.76 116.75 -1.99 1.14e+00 7.69e-01 3.05e+00 angle pdb=" CA ALA D 90 " pdb=" C ALA D 90 " pdb=" N ALA D 91 " ideal model delta sigma weight residual 114.76 116.71 -1.95 1.14e+00 7.69e-01 2.94e+00 angle pdb=" CA ALA C 90 " pdb=" C ALA C 90 " pdb=" N ALA C 91 " ideal model delta sigma weight residual 114.76 116.69 -1.93 1.14e+00 7.69e-01 2.86e+00 angle pdb=" CA ALA A 90 " pdb=" C ALA A 90 " pdb=" N ALA A 91 " ideal model delta sigma weight residual 114.76 116.69 -1.93 1.14e+00 7.69e-01 2.86e+00 angle pdb=" CA ALA E 90 " pdb=" C ALA E 90 " pdb=" N ALA E 91 " ideal model delta sigma weight residual 114.76 116.68 -1.92 1.14e+00 7.69e-01 2.84e+00 ... (remaining 3523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.21: 1350 13.21 - 26.41: 120 26.41 - 39.62: 36 39.62 - 52.82: 0 52.82 - 66.03: 12 Dihedral angle restraints: 1518 sinusoidal: 504 harmonic: 1014 Sorted by residual: dihedral pdb=" CA ASP B 98 " pdb=" CB ASP B 98 " pdb=" CG ASP B 98 " pdb=" OD1 ASP B 98 " ideal model delta sinusoidal sigma weight residual -30.00 -89.45 59.45 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP F 98 " pdb=" CB ASP F 98 " pdb=" CG ASP F 98 " pdb=" OD1 ASP F 98 " ideal model delta sinusoidal sigma weight residual -30.00 -89.44 59.44 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP C 98 " pdb=" CB ASP C 98 " pdb=" CG ASP C 98 " pdb=" OD1 ASP C 98 " ideal model delta sinusoidal sigma weight residual -30.00 -89.41 59.41 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 1515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 227 0.026 - 0.053: 128 0.053 - 0.079: 35 0.079 - 0.106: 37 0.106 - 0.132: 35 Chirality restraints: 462 Sorted by residual: chirality pdb=" CA VAL C 66 " pdb=" N VAL C 66 " pdb=" C VAL C 66 " pdb=" CB VAL C 66 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA VAL D 66 " pdb=" N VAL D 66 " pdb=" C VAL D 66 " pdb=" CB VAL D 66 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA VAL F 66 " pdb=" N VAL F 66 " pdb=" C VAL F 66 " pdb=" CB VAL F 66 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 459 not shown) Planarity restraints: 438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 68 " 0.003 2.00e-02 2.50e+03 6.10e-03 3.72e-01 pdb=" C GLY B 68 " -0.011 2.00e-02 2.50e+03 pdb=" O GLY B 68 " 0.004 2.00e-02 2.50e+03 pdb=" N ALA B 69 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 68 " -0.003 2.00e-02 2.50e+03 6.08e-03 3.70e-01 pdb=" C GLY A 68 " 0.011 2.00e-02 2.50e+03 pdb=" O GLY A 68 " -0.004 2.00e-02 2.50e+03 pdb=" N ALA A 69 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 68 " -0.003 2.00e-02 2.50e+03 6.04e-03 3.65e-01 pdb=" C GLY D 68 " 0.010 2.00e-02 2.50e+03 pdb=" O GLY D 68 " -0.004 2.00e-02 2.50e+03 pdb=" N ALA D 69 " -0.004 2.00e-02 2.50e+03 ... (remaining 435 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 716 2.82 - 3.34: 2357 3.34 - 3.86: 3650 3.86 - 4.38: 4096 4.38 - 4.90: 8597 Nonbonded interactions: 19416 Sorted by model distance: nonbonded pdb=" NE2 GLN E 62 " pdb=" OG1 THR E 64 " model vdw 2.295 2.520 nonbonded pdb=" NE2 GLN C 62 " pdb=" OG1 THR C 64 " model vdw 2.296 2.520 nonbonded pdb=" NE2 GLN F 62 " pdb=" OG1 THR F 64 " model vdw 2.296 2.520 nonbonded pdb=" NE2 GLN B 62 " pdb=" OG1 THR B 64 " model vdw 2.296 2.520 nonbonded pdb=" NE2 GLN D 62 " pdb=" OG1 THR D 64 " model vdw 2.296 2.520 ... (remaining 19411 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.700 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: 3.600 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.000 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:11.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 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 : 0.002 0.009 2610 Z= 0.120 Angle : 0.484 2.756 3528 Z= 0.293 Chirality : 0.051 0.132 462 Planarity : 0.001 0.006 438 Dihedral : 12.912 66.027 882 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % 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: -5.61 (0.29), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.27 (0.22), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.005 0.001 PHE C 94 TYR 0.009 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.287 Fit side-chains REVERT: B 46 GLU cc_start: 0.6694 (tt0) cc_final: 0.5943 (tp30) REVERT: A 46 GLU cc_start: 0.6393 (tt0) cc_final: 0.5827 (tp30) REVERT: A 57 GLU cc_start: 0.7224 (tt0) cc_final: 0.6981 (mt-10) REVERT: E 43 LYS cc_start: 0.7369 (tttt) cc_final: 0.7013 (mtpp) REVERT: E 46 GLU cc_start: 0.7164 (tt0) cc_final: 0.6744 (tt0) REVERT: C 43 LYS cc_start: 0.7382 (tttt) cc_final: 0.7090 (mtpm) REVERT: C 46 GLU cc_start: 0.6823 (tt0) cc_final: 0.6023 (tp30) REVERT: F 43 LYS cc_start: 0.7784 (tttt) cc_final: 0.7579 (ttmm) REVERT: F 46 GLU cc_start: 0.6978 (tt0) cc_final: 0.6701 (tt0) REVERT: D 46 GLU cc_start: 0.7069 (tt0) cc_final: 0.6471 (tp30) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.8764 time to fit residues: 60.5182 Evaluate side-chains 47 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 GLN E 62 GLN E 79 GLN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN D 62 GLN D 65 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2610 Z= 0.351 Angle : 0.575 3.628 3528 Z= 0.332 Chirality : 0.051 0.125 462 Planarity : 0.003 0.008 438 Dihedral : 5.060 13.959 378 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.59 % Favored : 75.41 % Rotamer: Outliers : 4.92 % Allowed : 12.88 % Favored : 82.20 % 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: -5.50 (0.30), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.18 (0.23), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.007 0.002 PHE A 94 TYR 0.013 0.004 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 49 time to evaluate : 0.277 Fit side-chains REVERT: B 46 GLU cc_start: 0.6737 (tt0) cc_final: 0.6188 (tp30) REVERT: A 46 GLU cc_start: 0.6518 (tt0) cc_final: 0.5880 (tm-30) REVERT: E 43 LYS cc_start: 0.7615 (tttt) cc_final: 0.7203 (mtpm) REVERT: E 46 GLU cc_start: 0.7212 (tt0) cc_final: 0.6671 (tp30) REVERT: C 43 LYS cc_start: 0.7600 (tttt) cc_final: 0.7394 (mtpp) REVERT: C 46 GLU cc_start: 0.7007 (tt0) cc_final: 0.6281 (tp30) REVERT: F 46 GLU cc_start: 0.7054 (tt0) cc_final: 0.6762 (tt0) REVERT: F 57 GLU cc_start: 0.7942 (tt0) cc_final: 0.7679 (tt0) REVERT: D 46 GLU cc_start: 0.7275 (tt0) cc_final: 0.6587 (tp30) REVERT: D 62 GLN cc_start: 0.7387 (tp-100) cc_final: 0.6930 (tm-30) outliers start: 13 outliers final: 9 residues processed: 57 average time/residue: 1.0009 time to fit residues: 58.6514 Evaluate side-chains 48 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain D residue 54 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 0.4980 chunk 10 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2610 Z= 0.258 Angle : 0.529 4.405 3528 Z= 0.300 Chirality : 0.050 0.127 462 Planarity : 0.002 0.006 438 Dihedral : 4.897 13.453 378 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.40 % Favored : 80.60 % Rotamer: Outliers : 6.44 % Allowed : 10.61 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.21 (0.31), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.96 (0.23), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 PHE 0.006 0.001 PHE A 94 TYR 0.010 0.003 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 46 time to evaluate : 0.281 Fit side-chains REVERT: B 46 GLU cc_start: 0.6708 (tt0) cc_final: 0.6119 (tp30) REVERT: A 46 GLU cc_start: 0.6662 (tt0) cc_final: 0.5770 (tm-30) REVERT: E 43 LYS cc_start: 0.7451 (tttt) cc_final: 0.7180 (mtpm) REVERT: E 46 GLU cc_start: 0.7203 (tt0) cc_final: 0.6549 (tm-30) REVERT: C 43 LYS cc_start: 0.7458 (tttt) cc_final: 0.7233 (mtpp) REVERT: C 46 GLU cc_start: 0.7076 (tt0) cc_final: 0.6326 (tp30) REVERT: F 46 GLU cc_start: 0.6961 (tt0) cc_final: 0.6671 (tt0) REVERT: F 57 GLU cc_start: 0.7989 (tt0) cc_final: 0.7771 (tt0) REVERT: F 92 THR cc_start: 0.7831 (m) cc_final: 0.7403 (p) REVERT: D 46 GLU cc_start: 0.7317 (tt0) cc_final: 0.6647 (tp30) REVERT: D 62 GLN cc_start: 0.7357 (tp-100) cc_final: 0.6955 (tm-30) outliers start: 17 outliers final: 12 residues processed: 60 average time/residue: 0.8722 time to fit residues: 54.0883 Evaluate side-chains 51 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.0470 chunk 31 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2610 Z= 0.211 Angle : 0.494 3.616 3528 Z= 0.280 Chirality : 0.049 0.128 462 Planarity : 0.002 0.004 438 Dihedral : 4.623 14.863 378 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.77 % Favored : 79.23 % Rotamer: Outliers : 5.30 % Allowed : 12.88 % Favored : 81.82 % 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: -4.99 (0.32), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 PHE 0.005 0.001 PHE B 94 TYR 0.008 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 49 time to evaluate : 0.296 Fit side-chains REVERT: B 46 GLU cc_start: 0.6639 (tt0) cc_final: 0.6107 (tp30) REVERT: A 46 GLU cc_start: 0.6674 (tt0) cc_final: 0.5798 (tm-30) REVERT: E 43 LYS cc_start: 0.7463 (tttt) cc_final: 0.7204 (mtpm) REVERT: E 46 GLU cc_start: 0.7193 (tt0) cc_final: 0.6479 (tp30) REVERT: E 92 THR cc_start: 0.7558 (m) cc_final: 0.7025 (p) REVERT: C 43 LYS cc_start: 0.7453 (tttt) cc_final: 0.7217 (mtpp) REVERT: C 46 GLU cc_start: 0.7079 (tt0) cc_final: 0.6323 (tp30) REVERT: F 46 GLU cc_start: 0.6966 (tt0) cc_final: 0.6669 (tt0) REVERT: F 57 GLU cc_start: 0.7984 (tt0) cc_final: 0.7773 (tt0) REVERT: F 92 THR cc_start: 0.7819 (m) cc_final: 0.7387 (p) REVERT: D 46 GLU cc_start: 0.7273 (tt0) cc_final: 0.6614 (tp30) REVERT: D 62 GLN cc_start: 0.7369 (tp-100) cc_final: 0.7022 (tm-30) outliers start: 14 outliers final: 10 residues processed: 60 average time/residue: 1.0044 time to fit residues: 61.9626 Evaluate side-chains 52 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.0970 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 31 optimal weight: 0.0000 chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 overall best weight: 3.2190 ------------------------------------------------------------------------------- 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: 0.7232 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2610 Z= 0.275 Angle : 0.539 3.691 3528 Z= 0.305 Chirality : 0.049 0.126 462 Planarity : 0.002 0.006 438 Dihedral : 4.843 15.325 378 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.40 % Favored : 77.60 % Rotamer: Outliers : 4.55 % Allowed : 14.77 % Favored : 80.68 % 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: -5.00 (0.32), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.006 0.002 PHE A 94 TYR 0.011 0.003 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 43 time to evaluate : 0.260 Fit side-chains REVERT: B 46 GLU cc_start: 0.6688 (tt0) cc_final: 0.6130 (tp30) REVERT: A 46 GLU cc_start: 0.6696 (tt0) cc_final: 0.5845 (tm-30) REVERT: E 43 LYS cc_start: 0.7482 (tttt) cc_final: 0.7221 (mtpm) REVERT: E 46 GLU cc_start: 0.7249 (tt0) cc_final: 0.6556 (tm-30) REVERT: C 43 LYS cc_start: 0.7465 (tttt) cc_final: 0.7214 (mtpp) REVERT: C 46 GLU cc_start: 0.7103 (tt0) cc_final: 0.6347 (tp30) REVERT: C 57 GLU cc_start: 0.7778 (tt0) cc_final: 0.7393 (tt0) REVERT: F 46 GLU cc_start: 0.7015 (tt0) cc_final: 0.6721 (tt0) REVERT: F 57 GLU cc_start: 0.7942 (tt0) cc_final: 0.7729 (tt0) REVERT: D 46 GLU cc_start: 0.7285 (tt0) cc_final: 0.6734 (tp30) REVERT: D 62 GLN cc_start: 0.7374 (tp-100) cc_final: 0.7090 (tm-30) outliers start: 12 outliers final: 12 residues processed: 54 average time/residue: 0.9088 time to fit residues: 50.5917 Evaluate side-chains 53 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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: 0.7214 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2610 Z= 0.233 Angle : 0.503 3.623 3528 Z= 0.284 Chirality : 0.049 0.127 462 Planarity : 0.002 0.005 438 Dihedral : 4.677 14.909 378 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.04 % Favored : 78.96 % Rotamer: Outliers : 3.79 % Allowed : 16.67 % Favored : 79.55 % 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: -4.89 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.005 0.001 PHE A 94 TYR 0.009 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 0.317 Fit side-chains REVERT: B 46 GLU cc_start: 0.6680 (tt0) cc_final: 0.6102 (tp30) REVERT: A 46 GLU cc_start: 0.6654 (tt0) cc_final: 0.5750 (tm-30) REVERT: E 43 LYS cc_start: 0.7467 (tttt) cc_final: 0.7178 (mtpm) REVERT: E 46 GLU cc_start: 0.7215 (tt0) cc_final: 0.6523 (tm-30) REVERT: C 43 LYS cc_start: 0.7452 (tttt) cc_final: 0.7221 (mtpm) REVERT: C 46 GLU cc_start: 0.7072 (tt0) cc_final: 0.6321 (tp30) REVERT: C 57 GLU cc_start: 0.7785 (tt0) cc_final: 0.7400 (tt0) REVERT: F 46 GLU cc_start: 0.6965 (tt0) cc_final: 0.6683 (tt0) REVERT: F 57 GLU cc_start: 0.7930 (tt0) cc_final: 0.7722 (tt0) REVERT: F 92 THR cc_start: 0.7801 (m) cc_final: 0.7413 (p) REVERT: D 46 GLU cc_start: 0.7215 (tt0) cc_final: 0.6684 (tp30) REVERT: D 62 GLN cc_start: 0.7375 (tp-100) cc_final: 0.7066 (tm-30) outliers start: 10 outliers final: 10 residues processed: 54 average time/residue: 0.9784 time to fit residues: 54.4511 Evaluate side-chains 51 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 9.9990 chunk 34 optimal weight: 0.0870 chunk 21 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 overall best weight: 1.4562 ------------------------------------------------------------------------------- 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: 0.7162 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2610 Z= 0.149 Angle : 0.440 3.800 3528 Z= 0.245 Chirality : 0.049 0.127 462 Planarity : 0.001 0.004 438 Dihedral : 4.197 13.039 378 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.85 % Favored : 84.15 % Rotamer: Outliers : 3.79 % Allowed : 17.05 % Favored : 79.17 % 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: -4.61 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.004 0.001 PHE A 94 TYR 0.005 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.359 Fit side-chains REVERT: B 46 GLU cc_start: 0.6727 (tt0) cc_final: 0.6027 (tp30) REVERT: A 46 GLU cc_start: 0.6685 (tt0) cc_final: 0.5846 (tp30) REVERT: E 43 LYS cc_start: 0.7440 (tttt) cc_final: 0.7142 (mtpm) REVERT: E 46 GLU cc_start: 0.7171 (tt0) cc_final: 0.6471 (tm-30) REVERT: E 92 THR cc_start: 0.7634 (m) cc_final: 0.7102 (p) REVERT: C 43 LYS cc_start: 0.7418 (tttt) cc_final: 0.7168 (mtpm) REVERT: C 46 GLU cc_start: 0.7063 (tt0) cc_final: 0.6176 (tp30) REVERT: C 57 GLU cc_start: 0.7790 (tt0) cc_final: 0.7289 (tt0) REVERT: F 46 GLU cc_start: 0.6937 (tt0) cc_final: 0.6642 (tt0) REVERT: F 92 THR cc_start: 0.7901 (m) cc_final: 0.7490 (p) REVERT: D 46 GLU cc_start: 0.7235 (tt0) cc_final: 0.6712 (tp30) REVERT: D 62 GLN cc_start: 0.7301 (tp-100) cc_final: 0.6948 (tm-30) outliers start: 10 outliers final: 9 residues processed: 55 average time/residue: 0.9147 time to fit residues: 51.9204 Evaluate side-chains 49 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 0.0060 chunk 25 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN A 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2610 Z= 0.107 Angle : 0.411 4.162 3528 Z= 0.226 Chirality : 0.050 0.137 462 Planarity : 0.001 0.016 438 Dihedral : 3.624 9.616 378 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 3.79 % Allowed : 18.56 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.37), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.003 0.001 PHE B 94 TYR 0.002 0.000 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.297 Fit side-chains REVERT: B 46 GLU cc_start: 0.6909 (tt0) cc_final: 0.6085 (tp30) REVERT: A 46 GLU cc_start: 0.6675 (tt0) cc_final: 0.5814 (tp30) REVERT: E 43 LYS cc_start: 0.7444 (tttt) cc_final: 0.7200 (mtpm) REVERT: E 46 GLU cc_start: 0.7242 (tt0) cc_final: 0.6788 (tt0) REVERT: E 92 THR cc_start: 0.7566 (m) cc_final: 0.7002 (p) REVERT: C 43 LYS cc_start: 0.7473 (tttt) cc_final: 0.7234 (mtpm) REVERT: C 46 GLU cc_start: 0.7039 (tt0) cc_final: 0.6108 (tp30) REVERT: C 57 GLU cc_start: 0.7718 (tt0) cc_final: 0.7160 (tt0) REVERT: F 46 GLU cc_start: 0.6921 (tt0) cc_final: 0.6647 (tt0) REVERT: F 92 THR cc_start: 0.7913 (m) cc_final: 0.7485 (p) REVERT: D 46 GLU cc_start: 0.7159 (tt0) cc_final: 0.6549 (tp30) outliers start: 10 outliers final: 6 residues processed: 59 average time/residue: 0.8497 time to fit residues: 51.7837 Evaluate side-chains 52 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 10.0000 chunk 30 optimal weight: 0.0270 chunk 32 optimal weight: 9.9990 chunk 21 optimal weight: 0.0060 chunk 34 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 overall best weight: 1.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2610 Z= 0.175 Angle : 0.455 5.226 3528 Z= 0.253 Chirality : 0.048 0.123 462 Planarity : 0.001 0.004 438 Dihedral : 3.969 11.610 378 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.85 % Favored : 84.15 % Rotamer: Outliers : 2.65 % Allowed : 18.94 % 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: -4.27 (0.37), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.004 0.001 PHE E 94 TYR 0.008 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.294 Fit side-chains REVERT: B 46 GLU cc_start: 0.6724 (tt0) cc_final: 0.6001 (tp30) REVERT: A 46 GLU cc_start: 0.6683 (tt0) cc_final: 0.5830 (tm-30) REVERT: E 43 LYS cc_start: 0.7475 (tttt) cc_final: 0.7229 (mtpm) REVERT: E 46 GLU cc_start: 0.7218 (tt0) cc_final: 0.6524 (tm-30) REVERT: E 92 THR cc_start: 0.7588 (m) cc_final: 0.7028 (p) REVERT: C 43 LYS cc_start: 0.7495 (tttt) cc_final: 0.7266 (mtpm) REVERT: C 46 GLU cc_start: 0.7063 (tt0) cc_final: 0.6317 (tp30) REVERT: C 57 GLU cc_start: 0.7704 (tt0) cc_final: 0.7189 (tt0) REVERT: F 46 GLU cc_start: 0.6992 (tt0) cc_final: 0.6716 (tt0) REVERT: F 92 THR cc_start: 0.7907 (m) cc_final: 0.7487 (p) REVERT: D 46 GLU cc_start: 0.7280 (tt0) cc_final: 0.6770 (tp30) outliers start: 7 outliers final: 6 residues processed: 53 average time/residue: 0.9255 time to fit residues: 50.6003 Evaluate side-chains 50 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 29 optimal weight: 0.0870 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2610 Z= 0.239 Angle : 0.514 5.516 3528 Z= 0.288 Chirality : 0.049 0.122 462 Planarity : 0.002 0.005 438 Dihedral : 4.405 14.090 378 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.85 % Favored : 81.15 % Rotamer: Outliers : 2.65 % Allowed : 18.18 % Favored : 79.17 % 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: -4.48 (0.36), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.005 0.001 PHE E 94 TYR 0.011 0.003 TYR D 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.293 Fit side-chains REVERT: B 46 GLU cc_start: 0.6642 (tt0) cc_final: 0.6072 (tp30) REVERT: A 46 GLU cc_start: 0.6721 (tt0) cc_final: 0.5827 (tm-30) REVERT: E 43 LYS cc_start: 0.7486 (tttt) cc_final: 0.7222 (mtpm) REVERT: E 46 GLU cc_start: 0.7193 (tt0) cc_final: 0.6516 (tm-30) REVERT: E 92 THR cc_start: 0.7576 (m) cc_final: 0.7031 (p) REVERT: C 43 LYS cc_start: 0.7458 (tttt) cc_final: 0.7218 (mtpm) REVERT: C 46 GLU cc_start: 0.7094 (tt0) cc_final: 0.6341 (tp30) REVERT: C 57 GLU cc_start: 0.7706 (tt0) cc_final: 0.7166 (tt0) REVERT: F 46 GLU cc_start: 0.7025 (tt0) cc_final: 0.6738 (tt0) REVERT: D 46 GLU cc_start: 0.7245 (tt0) cc_final: 0.6707 (tp30) outliers start: 7 outliers final: 6 residues processed: 49 average time/residue: 0.9470 time to fit residues: 47.8852 Evaluate side-chains 48 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 0.0670 chunk 1 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.162655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.119729 restraints weight = 2865.438| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.91 r_work: 0.3831 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2610 Z= 0.254 Angle : 0.524 4.814 3528 Z= 0.294 Chirality : 0.049 0.123 462 Planarity : 0.002 0.005 438 Dihedral : 4.568 14.405 378 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.31 % Favored : 78.69 % Rotamer: Outliers : 2.65 % Allowed : 18.18 % Favored : 79.17 % 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: -4.60 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.005 0.001 PHE E 94 TYR 0.012 0.003 TYR D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1512.12 seconds wall clock time: 27 minutes 28.61 seconds (1648.61 seconds total)