Starting phenix.real_space_refine on Mon Mar 11 13:08:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsl_12570/03_2024/7nsl_12570.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsl_12570/03_2024/7nsl_12570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsl_12570/03_2024/7nsl_12570.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsl_12570/03_2024/7nsl_12570.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsl_12570/03_2024/7nsl_12570.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsl_12570/03_2024/7nsl_12570.pdb" } resolution = 3.1 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= 1.000 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: 5 Type Number sf(0) Gaussians S 14 5.16 5 C 2667 2.51 5 N 679 2.21 5 O 910 1.98 5 H 4053 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 83": "OD1" <-> "OD2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "E TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 83": "OD1" <-> "OD2" Residue "E ASP 86": "OD1" <-> "OD2" Residue "F TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 83": "OD1" <-> "OD2" Residue "F ASP 86": "OD1" <-> "OD2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "B TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 83": "OD1" <-> "OD2" Residue "A ASP 86": "OD1" <-> "OD2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 83": "OD1" <-> "OD2" Residue "G ASP 86": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8323 Number of models: 1 Model: "" Number of chains: 7 Chain: "D" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1189 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Chain: "E" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1189 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Chain: "F" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1189 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Chain: "C" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1189 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Chain: "B" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1189 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Chain: "A" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1189 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Chain: "G" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1189 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Time building chain proxies: 4.45, per 1000 atoms: 0.53 Number of scatterers: 8323 At special positions: 0 Unit cell: (64.48, 98.8, 58.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 910 8.00 N 679 7.00 C 2667 6.00 H 4053 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 89 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 89 " distance=2.02 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 89 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 89 " distance=2.02 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: 7.14 Conformation dependent library (CDL) restraints added in 1.0 seconds 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1022 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 21 Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 34 Processing sheet with id=AA4, first strand: chain 'A' and resid 37 through 39 Processing sheet with id=AA5, first strand: chain 'A' and resid 43 through 44 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 43 through 44 current: chain 'B' and resid 43 through 44 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 43 through 44 current: chain 'C' and resid 43 through 44 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 43 through 44 current: chain 'D' and resid 43 through 44 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 43 through 44 current: chain 'E' and resid 43 through 44 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 43 through 44 current: chain 'F' and resid 43 through 44 No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 45 through 51 Processing sheet with id=AA7, first strand: chain 'A' and resid 70 through 74 Processing sheet with id=AA8, first strand: chain 'A' and resid 76 through 78 Processing sheet with id=AA9, first strand: chain 'A' and resid 88 through 89 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 88 through 89 current: chain 'B' and resid 88 through 89 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 88 through 89 current: chain 'C' and resid 88 through 89 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 88 through 89 current: chain 'D' and resid 88 through 89 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 88 through 89 current: chain 'E' and resid 88 through 89 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 88 through 89 current: chain 'F' and resid 88 through 89 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AB2, first strand: chain 'A' and resid 105 through 107 180 hydrogen bonds defined for protein. 540 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: 3.36 Time building geometry restraints manager: 7.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4053 1.03 - 1.23: 125 1.23 - 1.42: 1730 1.42 - 1.61: 2478 1.61 - 1.81: 14 Bond restraints: 8400 Sorted by residual: bond pdb=" CA ALA G 44 " pdb=" CB ALA G 44 " ideal model delta sigma weight residual 1.528 1.441 0.087 1.17e-02 7.31e+03 5.56e+01 bond pdb=" CA ALA A 44 " pdb=" CB ALA A 44 " ideal model delta sigma weight residual 1.528 1.441 0.087 1.17e-02 7.31e+03 5.56e+01 bond pdb=" CA ALA B 44 " pdb=" CB ALA B 44 " ideal model delta sigma weight residual 1.528 1.442 0.087 1.17e-02 7.31e+03 5.48e+01 bond pdb=" CA ALA E 44 " pdb=" CB ALA E 44 " ideal model delta sigma weight residual 1.528 1.442 0.087 1.17e-02 7.31e+03 5.47e+01 bond pdb=" CA ALA F 44 " pdb=" CB ALA F 44 " ideal model delta sigma weight residual 1.528 1.442 0.086 1.17e-02 7.31e+03 5.46e+01 ... (remaining 8395 not shown) Histogram of bond angle deviations from ideal: 100.94 - 107.59: 745 107.59 - 114.23: 9558 114.23 - 120.88: 2545 120.88 - 127.53: 2159 127.53 - 134.18: 50 Bond angle restraints: 15057 Sorted by residual: angle pdb=" CA GLY G 90 " pdb=" C GLY G 90 " pdb=" O GLY G 90 " ideal model delta sigma weight residual 120.91 114.30 6.61 6.90e-01 2.10e+00 9.18e+01 angle pdb=" CA GLY C 90 " pdb=" C GLY C 90 " pdb=" O GLY C 90 " ideal model delta sigma weight residual 120.91 114.34 6.57 6.90e-01 2.10e+00 9.06e+01 angle pdb=" CA GLY E 90 " pdb=" C GLY E 90 " pdb=" O GLY E 90 " ideal model delta sigma weight residual 120.91 114.35 6.56 6.90e-01 2.10e+00 9.03e+01 angle pdb=" CA GLY B 90 " pdb=" C GLY B 90 " pdb=" O GLY B 90 " ideal model delta sigma weight residual 120.91 114.36 6.55 6.90e-01 2.10e+00 9.01e+01 angle pdb=" CA GLY F 90 " pdb=" C GLY F 90 " pdb=" O GLY F 90 " ideal model delta sigma weight residual 120.91 114.37 6.54 6.90e-01 2.10e+00 8.97e+01 ... (remaining 15052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 3444 16.17 - 32.34: 413 32.34 - 48.51: 105 48.51 - 64.68: 91 64.68 - 80.86: 7 Dihedral angle restraints: 4060 sinusoidal: 2163 harmonic: 1897 Sorted by residual: dihedral pdb=" N LEU F 97 " pdb=" CA LEU F 97 " pdb=" CB LEU F 97 " pdb=" CG LEU F 97 " ideal model delta sinusoidal sigma weight residual -60.00 -113.63 53.63 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" N LEU C 97 " pdb=" CA LEU C 97 " pdb=" CB LEU C 97 " pdb=" CG LEU C 97 " ideal model delta sinusoidal sigma weight residual -60.00 -113.61 53.61 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" N LEU B 97 " pdb=" CA LEU B 97 " pdb=" CB LEU B 97 " pdb=" CG LEU B 97 " ideal model delta sinusoidal sigma weight residual -60.00 -113.61 53.61 3 1.50e+01 4.44e-03 9.22e+00 ... (remaining 4057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 390 0.056 - 0.111: 188 0.111 - 0.167: 67 0.167 - 0.222: 34 0.222 - 0.278: 14 Chirality restraints: 693 Sorted by residual: chirality pdb=" CA LEU A 47 " pdb=" N LEU A 47 " pdb=" C LEU A 47 " pdb=" CB LEU A 47 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA LEU B 47 " pdb=" N LEU B 47 " pdb=" C LEU B 47 " pdb=" CB LEU B 47 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA LEU F 47 " pdb=" N LEU F 47 " pdb=" C LEU F 47 " pdb=" CB LEU F 47 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 690 not shown) Planarity restraints: 1309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN E 16 " -0.240 2.00e-02 2.50e+03 3.43e-01 1.77e+03 pdb=" CD GLN E 16 " 0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN E 16 " 0.236 2.00e-02 2.50e+03 pdb=" NE2 GLN E 16 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN E 16 " 0.544 2.00e-02 2.50e+03 pdb="HE22 GLN E 16 " -0.546 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN G 16 " -0.240 2.00e-02 2.50e+03 3.43e-01 1.77e+03 pdb=" CD GLN G 16 " 0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN G 16 " 0.236 2.00e-02 2.50e+03 pdb=" NE2 GLN G 16 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN G 16 " 0.544 2.00e-02 2.50e+03 pdb="HE22 GLN G 16 " -0.546 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 16 " -0.240 2.00e-02 2.50e+03 3.43e-01 1.77e+03 pdb=" CD GLN D 16 " 0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN D 16 " 0.236 2.00e-02 2.50e+03 pdb=" NE2 GLN D 16 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN D 16 " 0.544 2.00e-02 2.50e+03 pdb="HE22 GLN D 16 " -0.546 2.00e-02 2.50e+03 ... (remaining 1306 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 427 2.18 - 2.78: 16305 2.78 - 3.39: 22336 3.39 - 3.99: 32827 3.99 - 4.60: 47613 Nonbonded interactions: 119508 Sorted by model distance: nonbonded pdb=" HG1 THR A 81 " pdb=" OD1 ASP A 83 " model vdw 1.572 1.850 nonbonded pdb=" HG1 THR E 81 " pdb=" OD1 ASP E 83 " model vdw 1.573 1.850 nonbonded pdb=" HG1 THR F 81 " pdb=" OD1 ASP F 83 " model vdw 1.573 1.850 nonbonded pdb=" HG1 THR G 81 " pdb=" OD1 ASP G 83 " model vdw 1.573 1.850 nonbonded pdb=" HG1 THR D 81 " pdb=" OD1 ASP D 83 " model vdw 1.573 1.850 ... (remaining 119503 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' selection = chain 'G' } 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: 0.760 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: 0.130 Extract box with map and model: 3.960 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 32.940 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 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 : 0.012 0.087 4347 Z= 0.814 Angle : 1.845 8.934 5929 Z= 1.282 Chirality : 0.084 0.278 693 Planarity : 0.014 0.039 749 Dihedral : 14.483 80.856 1442 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % 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: -5.51 (0.17), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.19 (0.13), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 36 PHE 0.018 0.006 PHE C 101 TYR 0.024 0.002 TYR E 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 38 GLN cc_start: 0.9084 (pt0) cc_final: 0.8778 (pt0) REVERT: C 48 LEU cc_start: 0.8864 (mp) cc_final: 0.8451 (mp) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2487 time to fit residues: 65.5934 Evaluate side-chains 153 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7898 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4347 Z= 0.220 Angle : 0.644 3.949 5929 Z= 0.345 Chirality : 0.046 0.157 693 Planarity : 0.004 0.023 749 Dihedral : 6.449 16.502 616 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.55 % Allowed : 15.37 % Favored : 80.09 % 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: -4.92 (0.19), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.15), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 36 PHE 0.015 0.003 PHE E 101 TYR 0.011 0.001 TYR E 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 162 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 38 GLN cc_start: 0.9240 (pt0) cc_final: 0.8989 (pt0) REVERT: C 84 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6441 (tt0) outliers start: 21 outliers final: 16 residues processed: 166 average time/residue: 0.2529 time to fit residues: 56.0027 Evaluate side-chains 171 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 86 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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: 0.8104 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 4347 Z= 0.457 Angle : 0.739 6.768 5929 Z= 0.389 Chirality : 0.047 0.145 693 Planarity : 0.004 0.024 749 Dihedral : 6.323 15.749 616 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 5.84 % Allowed : 15.80 % Favored : 78.35 % 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: -4.34 (0.23), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.18), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 92 PHE 0.040 0.008 PHE C 101 TYR 0.018 0.002 TYR B 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: C 101 PHE cc_start: 0.8719 (m-80) cc_final: 0.8229 (m-80) outliers start: 27 outliers final: 18 residues processed: 151 average time/residue: 0.3014 time to fit residues: 59.5329 Evaluate side-chains 153 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain G residue 40 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.8093 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4347 Z= 0.237 Angle : 0.623 4.753 5929 Z= 0.329 Chirality : 0.044 0.142 693 Planarity : 0.003 0.028 749 Dihedral : 6.119 17.042 616 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.98 % Allowed : 21.43 % Favored : 73.59 % 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: -4.21 (0.24), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.18), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 92 PHE 0.019 0.004 PHE E 101 TYR 0.014 0.001 TYR B 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: C 46 LYS cc_start: 0.8361 (ttmt) cc_final: 0.8089 (ttmt) REVERT: B 84 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6667 (tt0) outliers start: 23 outliers final: 17 residues processed: 145 average time/residue: 0.2858 time to fit residues: 54.7949 Evaluate side-chains 154 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 48 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 48 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.8103 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4347 Z= 0.232 Angle : 0.599 6.418 5929 Z= 0.312 Chirality : 0.044 0.135 693 Planarity : 0.003 0.028 749 Dihedral : 5.945 16.931 616 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 4.98 % Allowed : 21.86 % Favored : 73.16 % 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: -4.14 (0.25), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 92 PHE 0.022 0.003 PHE F 101 TYR 0.014 0.001 TYR B 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 139 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: B 84 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6682 (tt0) outliers start: 23 outliers final: 17 residues processed: 143 average time/residue: 0.2715 time to fit residues: 51.0025 Evaluate side-chains 148 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 38 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 0.0010 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- 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: 0.8125 moved from start: 0.5870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4347 Z= 0.272 Angle : 0.606 4.363 5929 Z= 0.319 Chirality : 0.044 0.136 693 Planarity : 0.003 0.028 749 Dihedral : 5.945 16.418 616 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.76 % Allowed : 24.03 % Favored : 71.21 % 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: -4.16 (0.25), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 92 PHE 0.008 0.002 PHE E 101 TYR 0.013 0.001 TYR B 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 0.639 Fit side-chains outliers start: 22 outliers final: 20 residues processed: 132 average time/residue: 0.2869 time to fit residues: 49.4805 Evaluate side-chains 146 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain G residue 28 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 0.0040 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.5952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4347 Z= 0.173 Angle : 0.565 4.253 5929 Z= 0.297 Chirality : 0.044 0.135 693 Planarity : 0.003 0.028 749 Dihedral : 5.808 16.781 616 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 4.55 % Allowed : 24.03 % Favored : 71.43 % 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: -4.08 (0.25), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP G 92 PHE 0.007 0.001 PHE E 101 TYR 0.019 0.001 TYR B 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 0.612 Fit side-chains REVERT: E 35 SER cc_start: 0.8796 (t) cc_final: 0.8578 (t) outliers start: 21 outliers final: 18 residues processed: 136 average time/residue: 0.2815 time to fit residues: 49.8504 Evaluate side-chains 150 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain G residue 28 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 0.0010 chunk 51 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.6085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4347 Z= 0.247 Angle : 0.585 4.004 5929 Z= 0.308 Chirality : 0.044 0.133 693 Planarity : 0.003 0.028 749 Dihedral : 5.831 16.089 616 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.55 % Allowed : 23.81 % Favored : 71.65 % 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: -4.11 (0.25), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 92 PHE 0.005 0.001 PHE E 101 TYR 0.017 0.001 TYR B 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 0.729 Fit side-chains REVERT: E 35 SER cc_start: 0.8835 (t) cc_final: 0.8615 (t) outliers start: 21 outliers final: 19 residues processed: 134 average time/residue: 0.2788 time to fit residues: 48.6520 Evaluate side-chains 147 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain G residue 28 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 0.0270 chunk 44 optimal weight: 0.6980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.6175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4347 Z= 0.162 Angle : 0.560 4.276 5929 Z= 0.294 Chirality : 0.043 0.134 693 Planarity : 0.003 0.027 749 Dihedral : 5.725 16.329 616 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 4.76 % Allowed : 23.81 % Favored : 71.43 % 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: -4.06 (0.25), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 92 PHE 0.005 0.001 PHE E 101 TYR 0.015 0.001 TYR B 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 0.734 Fit side-chains REVERT: E 35 SER cc_start: 0.8790 (t) cc_final: 0.8575 (t) outliers start: 22 outliers final: 19 residues processed: 133 average time/residue: 0.2849 time to fit residues: 49.7543 Evaluate side-chains 147 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.6262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4347 Z= 0.205 Angle : 0.566 4.110 5929 Z= 0.296 Chirality : 0.043 0.132 693 Planarity : 0.003 0.028 749 Dihedral : 5.702 15.409 616 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.33 % Allowed : 24.46 % Favored : 71.21 % 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: -4.10 (0.25), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 92 PHE 0.004 0.001 PHE E 101 TYR 0.015 0.001 TYR B 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 0.704 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 18 residues processed: 131 average time/residue: 0.2865 time to fit residues: 48.8657 Evaluate side-chains 142 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.121773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.107841 restraints weight = 18438.737| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.73 r_work: 0.3670 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.6381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 4347 Z= 0.366 Angle : 0.619 3.993 5929 Z= 0.327 Chirality : 0.044 0.138 693 Planarity : 0.003 0.028 749 Dihedral : 5.863 16.390 616 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 4.11 % Allowed : 25.11 % Favored : 70.78 % 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: -4.17 (0.24), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 36 PHE 0.006 0.001 PHE G 101 TYR 0.017 0.002 TYR B 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3316.13 seconds wall clock time: 58 minutes 56.43 seconds (3536.43 seconds total)