Starting phenix.real_space_refine on Wed Oct 9 13:28:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v48_31703/10_2024/7v48_31703.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v48_31703/10_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_31703/10_2024/7v48_31703.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v48_31703/10_2024/7v48_31703.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v48_31703/10_2024/7v48_31703.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v48_31703/10_2024/7v48_31703.cif" } 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. Time to flip 18 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 2598 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 1.69, per 1000 atoms: 0.65 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 364.5 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: 0.32 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: 0.49 Time building geometry restraints manager: 0.70 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: 0.00 - 0.55: 2848 0.55 - 1.10: 539 1.10 - 1.65: 103 1.65 - 2.21: 32 2.21 - 2.76: 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 3.120 nonbonded pdb=" NE2 GLN C 62 " pdb=" OG1 THR C 64 " model vdw 2.296 3.120 nonbonded pdb=" NE2 GLN F 62 " pdb=" OG1 THR F 64 " model vdw 2.296 3.120 nonbonded pdb=" NE2 GLN B 62 " pdb=" OG1 THR B 64 " model vdw 2.296 3.120 nonbonded pdb=" NE2 GLN D 62 " pdb=" OG1 THR D 64 " model vdw 2.296 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.810 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.000 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:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.800 ------------------------------------------------------------------------------- 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 : 0.290 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: 0.8731 time to fit residues: 60.3150 Evaluate side-chains 47 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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: 8.9990 chunk 27 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN E 79 GLN C 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2610 Z= 0.332 Angle : 0.568 3.653 3528 Z= 0.327 Chirality : 0.051 0.124 462 Planarity : 0.003 0.008 438 Dihedral : 5.101 15.265 378 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.95 % Favored : 80.05 % Rotamer: Outliers : 5.68 % Allowed : 9.47 % Favored : 84.85 % 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: -5.37 (0.30), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.09 (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 B 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 64 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 49 time to evaluate : 0.273 Fit side-chains REVERT: B 46 GLU cc_start: 0.6798 (tt0) cc_final: 0.6249 (tp30) REVERT: A 46 GLU cc_start: 0.6749 (tt0) cc_final: 0.5906 (tm-30) REVERT: A 57 GLU cc_start: 0.7307 (tt0) cc_final: 0.7092 (mt-10) REVERT: A 92 THR cc_start: 0.7448 (m) cc_final: 0.7105 (p) REVERT: E 43 LYS cc_start: 0.7620 (tttt) cc_final: 0.7368 (mtpm) REVERT: E 46 GLU cc_start: 0.7352 (tt0) cc_final: 0.6637 (tm-30) REVERT: E 92 THR cc_start: 0.7517 (m) cc_final: 0.7019 (p) REVERT: C 43 LYS cc_start: 0.7586 (tttt) cc_final: 0.7361 (mtpm) REVERT: C 46 GLU cc_start: 0.7064 (tt0) cc_final: 0.6457 (tp30) REVERT: F 46 GLU cc_start: 0.7004 (tt0) cc_final: 0.6709 (tt0) REVERT: F 57 GLU cc_start: 0.7931 (tt0) cc_final: 0.7663 (tt0) REVERT: D 46 GLU cc_start: 0.7283 (tt0) cc_final: 0.6686 (tp30) REVERT: D 62 GLN cc_start: 0.7392 (tp40) cc_final: 0.6981 (tm-30) outliers start: 15 outliers final: 9 residues processed: 61 average time/residue: 1.0828 time to fit residues: 67.8920 Evaluate side-chains 48 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain E residue 72 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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: 0.7190 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2610 Z= 0.155 Angle : 0.466 4.104 3528 Z= 0.261 Chirality : 0.050 0.128 462 Planarity : 0.002 0.005 438 Dihedral : 4.427 12.696 378 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.30 % Favored : 87.70 % Rotamer: Outliers : 3.79 % Allowed : 12.12 % Favored : 84.09 % 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: -4.91 (0.32), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.24), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.005 0.001 PHE A 94 TYR 0.006 0.002 TYR B 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 56 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.330 Fit side-chains REVERT: B 46 GLU cc_start: 0.6708 (tt0) cc_final: 0.6187 (tp30) REVERT: A 46 GLU cc_start: 0.6711 (tt0) cc_final: 0.5869 (tp30) REVERT: A 57 GLU cc_start: 0.7399 (tt0) cc_final: 0.7187 (mt-10) REVERT: A 92 THR cc_start: 0.7406 (m) cc_final: 0.7097 (p) REVERT: E 43 LYS cc_start: 0.7442 (tttt) cc_final: 0.7088 (mtpm) REVERT: E 46 GLU cc_start: 0.7193 (tt0) cc_final: 0.6568 (tp30) REVERT: C 46 GLU cc_start: 0.7163 (tt0) cc_final: 0.6213 (tp30) REVERT: F 46 GLU cc_start: 0.6916 (tt0) cc_final: 0.6612 (tt0) REVERT: F 92 THR cc_start: 0.7928 (m) cc_final: 0.7427 (p) REVERT: D 46 GLU cc_start: 0.7249 (tt0) cc_final: 0.6604 (tp30) REVERT: D 62 GLN cc_start: 0.7441 (tp40) cc_final: 0.6947 (tm-30) outliers start: 10 outliers final: 7 residues processed: 55 average time/residue: 1.1329 time to fit residues: 64.2205 Evaluate side-chains 46 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain E residue 72 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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: 0.7242 moved from start: 0.2033 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= 0.288 Angle : 0.541 4.032 3528 Z= 0.307 Chirality : 0.050 0.125 462 Planarity : 0.003 0.008 438 Dihedral : 4.781 14.808 378 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.67 % Favored : 80.33 % Rotamer: Outliers : 5.30 % Allowed : 13.26 % Favored : 81.44 % 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: -4.97 (0.32), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.24), 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 0.012 0.003 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 54 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 40 time to evaluate : 0.373 Fit side-chains REVERT: B 46 GLU cc_start: 0.6803 (tt0) cc_final: 0.6200 (tp30) REVERT: A 46 GLU cc_start: 0.6720 (tt0) cc_final: 0.5903 (tm-30) REVERT: A 57 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7068 (mt-10) REVERT: A 92 THR cc_start: 0.7380 (m) cc_final: 0.7155 (p) REVERT: E 43 LYS cc_start: 0.7520 (tttt) cc_final: 0.7177 (mtpm) REVERT: E 46 GLU cc_start: 0.7314 (tt0) cc_final: 0.6444 (tp30) REVERT: C 46 GLU cc_start: 0.7080 (tt0) cc_final: 0.6474 (tp30) REVERT: F 46 GLU cc_start: 0.6981 (tt0) cc_final: 0.6684 (tt0) REVERT: F 92 THR cc_start: 0.7916 (m) cc_final: 0.7461 (p) REVERT: D 43 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7706 (mtpp) REVERT: D 46 GLU cc_start: 0.7314 (tt0) cc_final: 0.6765 (tp30) REVERT: D 62 GLN cc_start: 0.7357 (tp40) cc_final: 0.7055 (tm-30) outliers start: 14 outliers final: 10 residues processed: 52 average time/residue: 1.0604 time to fit residues: 56.8794 Evaluate side-chains 50 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain E residue 72 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 43 LYS Chi-restraints excluded: chain D residue 87 SER 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: 0.5980 chunk 14 optimal weight: 7.9990 chunk 29 optimal weight: 0.1980 chunk 24 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 2610 Z= 0.379 Angle : 0.615 4.522 3528 Z= 0.353 Chirality : 0.051 0.124 462 Planarity : 0.003 0.010 438 Dihedral : 5.304 15.957 378 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.68 % Favored : 77.32 % Rotamer: Outliers : 3.79 % Allowed : 15.91 % Favored : 80.30 % 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: -5.25 (0.30), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.23), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS B 50 PHE 0.008 0.002 PHE A 94 TYR 0.015 0.004 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 54 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.306 Fit side-chains REVERT: B 46 GLU cc_start: 0.6798 (tt0) cc_final: 0.6229 (tp30) REVERT: B 62 GLN cc_start: 0.7472 (tp40) cc_final: 0.7112 (tm-30) REVERT: A 46 GLU cc_start: 0.6754 (tt0) cc_final: 0.5911 (tm-30) REVERT: A 57 GLU cc_start: 0.7505 (tt0) cc_final: 0.7228 (mt-10) REVERT: E 43 LYS cc_start: 0.7587 (tttt) cc_final: 0.7246 (mtpm) REVERT: E 46 GLU cc_start: 0.7393 (tt0) cc_final: 0.6637 (tm-30) REVERT: E 54 THR cc_start: 0.8606 (m) cc_final: 0.8403 (m) REVERT: E 92 THR cc_start: 0.7500 (m) cc_final: 0.7008 (p) REVERT: C 46 GLU cc_start: 0.7167 (tt0) cc_final: 0.6419 (tp30) REVERT: F 46 GLU cc_start: 0.7013 (tt0) cc_final: 0.6465 (tm-30) REVERT: F 92 THR cc_start: 0.7860 (m) cc_final: 0.7464 (p) REVERT: D 43 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7663 (mtpp) REVERT: D 46 GLU cc_start: 0.7295 (tt0) cc_final: 0.6740 (tp30) REVERT: D 62 GLN cc_start: 0.7281 (tp40) cc_final: 0.6397 (tp40) outliers start: 10 outliers final: 9 residues processed: 53 average time/residue: 1.0083 time to fit residues: 55.0553 Evaluate side-chains 49 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 THR 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 72 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 0.1980 chunk 16 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 0.0770 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2610 Z= 0.135 Angle : 0.456 4.259 3528 Z= 0.253 Chirality : 0.050 0.126 462 Planarity : 0.001 0.007 438 Dihedral : 4.402 14.413 378 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.30 % Favored : 87.70 % Rotamer: Outliers : 3.03 % Allowed : 17.42 % 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: -4.74 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.004 0.001 PHE B 94 TYR 0.005 0.001 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 49 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.328 Fit side-chains REVERT: B 46 GLU cc_start: 0.6841 (tt0) cc_final: 0.6275 (tp30) REVERT: A 46 GLU cc_start: 0.6671 (tt0) cc_final: 0.5773 (tm-30) REVERT: A 57 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7046 (mt-10) REVERT: E 43 LYS cc_start: 0.7448 (tttt) cc_final: 0.7127 (mtpm) REVERT: E 46 GLU cc_start: 0.7171 (tt0) cc_final: 0.6380 (tp30) REVERT: C 46 GLU cc_start: 0.7211 (tt0) cc_final: 0.6392 (tp30) REVERT: F 46 GLU cc_start: 0.6935 (tt0) cc_final: 0.6624 (tt0) REVERT: F 92 THR cc_start: 0.7891 (m) cc_final: 0.7479 (p) REVERT: D 46 GLU cc_start: 0.7128 (tt0) cc_final: 0.6697 (tp30) REVERT: D 62 GLN cc_start: 0.7333 (tp40) cc_final: 0.6984 (tm-30) outliers start: 8 outliers final: 6 residues processed: 47 average time/residue: 1.1053 time to fit residues: 53.5052 Evaluate side-chains 44 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F 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: 9.9990 chunk 29 optimal weight: 0.0020 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 overall best weight: 1.7594 ------------------------------------------------------------------------------- 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: 0.7171 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2610 Z= 0.172 Angle : 0.459 4.466 3528 Z= 0.255 Chirality : 0.049 0.123 462 Planarity : 0.002 0.005 438 Dihedral : 4.278 13.581 378 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.21 % Favored : 85.79 % Rotamer: Outliers : 4.17 % Allowed : 15.53 % Favored : 80.30 % 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: -4.56 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.004 0.001 PHE E 94 TYR 0.007 0.002 TYR C 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 52 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 41 time to evaluate : 0.279 Fit side-chains REVERT: B 46 GLU cc_start: 0.6763 (tt0) cc_final: 0.6227 (tp30) REVERT: A 46 GLU cc_start: 0.6729 (tt0) cc_final: 0.5878 (tm-30) REVERT: A 57 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7167 (mt-10) REVERT: E 43 LYS cc_start: 0.7489 (tttt) cc_final: 0.7144 (mtpm) REVERT: E 46 GLU cc_start: 0.7232 (tt0) cc_final: 0.6409 (tp30) REVERT: C 46 GLU cc_start: 0.7189 (tt0) cc_final: 0.6363 (tp30) REVERT: F 46 GLU cc_start: 0.6951 (tt0) cc_final: 0.6652 (tt0) REVERT: F 92 THR cc_start: 0.7885 (m) cc_final: 0.7465 (p) REVERT: D 46 GLU cc_start: 0.7133 (tt0) cc_final: 0.6698 (tp30) REVERT: D 62 GLN cc_start: 0.7245 (tp40) cc_final: 0.6916 (tm-30) outliers start: 11 outliers final: 8 residues processed: 51 average time/residue: 1.0107 time to fit residues: 53.2103 Evaluate side-chains 46 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain A residue 57 GLU 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 F residue 37 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F 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: 8.9990 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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: 0.7253 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 2610 Z= 0.388 Angle : 0.617 4.867 3528 Z= 0.351 Chirality : 0.051 0.123 462 Planarity : 0.003 0.010 438 Dihedral : 5.126 16.330 378 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.40 % Favored : 77.60 % Rotamer: Outliers : 4.55 % Allowed : 15.91 % 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: -5.05 (0.31), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.24), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS B 50 PHE 0.008 0.002 PHE E 94 TYR 0.017 0.004 TYR D 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 48 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 36 time to evaluate : 0.243 Fit side-chains REVERT: B 46 GLU cc_start: 0.6797 (tt0) cc_final: 0.6229 (tp30) REVERT: A 46 GLU cc_start: 0.6797 (tt0) cc_final: 0.5947 (tm-30) REVERT: A 57 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7228 (mt-10) REVERT: E 43 LYS cc_start: 0.7635 (tttt) cc_final: 0.7217 (mtpm) REVERT: E 46 GLU cc_start: 0.7364 (tt0) cc_final: 0.6497 (tp30) REVERT: E 54 THR cc_start: 0.8536 (m) cc_final: 0.8328 (m) REVERT: C 46 GLU cc_start: 0.7122 (tt0) cc_final: 0.6556 (tp30) REVERT: F 46 GLU cc_start: 0.6982 (tt0) cc_final: 0.6449 (tm-30) REVERT: F 92 THR cc_start: 0.7843 (m) cc_final: 0.7453 (p) REVERT: D 43 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7772 (mtpp) REVERT: D 46 GLU cc_start: 0.7239 (tt0) cc_final: 0.6726 (tp30) outliers start: 12 outliers final: 9 residues processed: 47 average time/residue: 1.0791 time to fit residues: 52.2068 Evaluate side-chains 44 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 33 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain A residue 57 GLU 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 43 LYS 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: 0.0470 chunk 32 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- 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: 0.7191 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2610 Z= 0.206 Angle : 0.508 5.234 3528 Z= 0.282 Chirality : 0.050 0.126 462 Planarity : 0.002 0.006 438 Dihedral : 4.633 15.305 378 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.75 % Favored : 85.25 % Rotamer: Outliers : 4.55 % Allowed : 17.80 % 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: -4.76 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (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 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 47 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 35 time to evaluate : 0.309 Fit side-chains REVERT: B 46 GLU cc_start: 0.6785 (tt0) cc_final: 0.6260 (tp30) REVERT: A 46 GLU cc_start: 0.6739 (tt0) cc_final: 0.5888 (tm-30) REVERT: A 57 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7081 (mt-10) REVERT: E 43 LYS cc_start: 0.7461 (tttt) cc_final: 0.7233 (mtpm) REVERT: E 46 GLU cc_start: 0.7277 (tt0) cc_final: 0.6566 (tm-30) REVERT: C 46 GLU cc_start: 0.7262 (tt0) cc_final: 0.6470 (tp30) REVERT: F 46 GLU cc_start: 0.6971 (tt0) cc_final: 0.6670 (tt0) REVERT: F 92 THR cc_start: 0.7882 (m) cc_final: 0.7492 (p) REVERT: D 46 GLU cc_start: 0.7143 (tt0) cc_final: 0.6688 (tp30) outliers start: 12 outliers final: 8 residues processed: 46 average time/residue: 1.0775 time to fit residues: 51.0872 Evaluate side-chains 42 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain A residue 57 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 29 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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: 0.7197 moved from start: 0.2398 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= 0.236 Angle : 0.534 5.330 3528 Z= 0.296 Chirality : 0.049 0.124 462 Planarity : 0.002 0.005 438 Dihedral : 4.623 15.409 378 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.21 % Favored : 82.79 % Rotamer: Outliers : 4.17 % Allowed : 17.42 % 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: -4.72 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.006 0.001 PHE E 94 TYR 0.010 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 46 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 35 time to evaluate : 0.379 Fit side-chains REVERT: B 46 GLU cc_start: 0.6779 (tt0) cc_final: 0.6246 (tp30) REVERT: A 46 GLU cc_start: 0.6712 (tt0) cc_final: 0.5846 (tm-30) REVERT: A 57 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7187 (mt-10) REVERT: E 43 LYS cc_start: 0.7493 (tttt) cc_final: 0.7176 (mtpm) REVERT: E 46 GLU cc_start: 0.7320 (tt0) cc_final: 0.6592 (tm-30) REVERT: C 46 GLU cc_start: 0.7256 (tt0) cc_final: 0.6465 (tp30) REVERT: F 46 GLU cc_start: 0.6954 (tt0) cc_final: 0.6665 (tt0) REVERT: F 92 THR cc_start: 0.7882 (m) cc_final: 0.7488 (p) REVERT: D 46 GLU cc_start: 0.7199 (tt0) cc_final: 0.6738 (tp30) outliers start: 11 outliers final: 9 residues processed: 45 average time/residue: 1.0546 time to fit residues: 49.1278 Evaluate side-chains 44 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 34 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain A residue 57 GLU 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 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 0.0060 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.170122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.126422 restraints weight = 2719.654| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 2.87 r_work: 0.3939 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2610 Z= 0.129 Angle : 0.453 5.418 3528 Z= 0.244 Chirality : 0.049 0.123 462 Planarity : 0.001 0.005 438 Dihedral : 3.994 11.392 378 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % 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: -4.39 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.004 0.001 PHE E 94 TYR 0.004 0.001 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1471.53 seconds wall clock time: 28 minutes 55.41 seconds (1735.41 seconds total)