Starting phenix.real_space_refine on Fri Dec 8 12:13:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsl_12570/12_2023/7nsl_12570.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsl_12570/12_2023/7nsl_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_12570/12_2023/7nsl_12570.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsl_12570/12_2023/7nsl_12570.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsl_12570/12_2023/7nsl_12570.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsl_12570/12_2023/7nsl_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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 3.87, per 1000 atoms: 0.46 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: 6.74 Conformation dependent library (CDL) restraints added in 921.9 milliseconds 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: 0.82 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: 3.01 Time building geometry restraints manager: 7.04 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: 3353 16.17 - 32.34: 371 32.34 - 48.51: 77 48.51 - 64.68: 63 64.68 - 80.86: 7 Dihedral angle restraints: 3871 sinusoidal: 1974 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 3868 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: 0.720 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: 0.140 Extract box with map and model: 3.950 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 30.190 Find NCS groups from input model: 0.410 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.320 ------------------------------------------------------------------------------- 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 : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2341 time to fit residues: 62.1873 Evaluate side-chains 152 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.690 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8068 ------------------------------------------------------------------------------- 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: 1.9990 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7894 moved from start: 0.3316 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= 0.208 Angle : 0.639 3.963 5929 Z= 0.342 Chirality : 0.045 0.156 693 Planarity : 0.004 0.023 749 Dihedral : 6.417 16.317 616 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.76 % Allowed : 15.58 % Favored : 79.65 % 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: -4.94 (0.19), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.15), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 36 PHE 0.015 0.003 PHE E 101 TYR 0.012 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 184 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 162 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 17 residues processed: 167 average time/residue: 0.2501 time to fit residues: 55.5643 Evaluate side-chains 171 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 0.633 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1100 time to fit residues: 3.9522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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: 0.8139 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 4347 Z= 0.518 Angle : 0.791 6.026 5929 Z= 0.420 Chirality : 0.049 0.139 693 Planarity : 0.004 0.027 749 Dihedral : 6.473 17.824 616 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 3.25 % Allowed : 17.97 % Favored : 78.79 % 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: -4.37 (0.23), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.18), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP G 36 PHE 0.033 0.007 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 154 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 139 time to evaluate : 0.686 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 144 average time/residue: 0.2843 time to fit residues: 53.1194 Evaluate side-chains 140 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 131 time to evaluate : 0.726 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1165 time to fit residues: 2.5575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 48 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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: 0.8089 moved from start: 0.5406 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= 0.191 Angle : 0.617 5.018 5929 Z= 0.325 Chirality : 0.044 0.144 693 Planarity : 0.003 0.027 749 Dihedral : 6.148 18.587 616 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.81 % Allowed : 21.43 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.24), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP G 92 PHE 0.021 0.004 PHE F 101 TYR 0.012 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 154 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 141 time to evaluate : 0.666 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 145 average time/residue: 0.2726 time to fit residues: 51.9499 Evaluate side-chains 140 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 0.682 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1185 time to fit residues: 2.3761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.0370 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: 0.8060 ------------------------------------------------------------------------------- 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: 0.8099 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4347 Z= 0.214 Angle : 0.595 5.454 5929 Z= 0.310 Chirality : 0.044 0.133 693 Planarity : 0.003 0.027 749 Dihedral : 5.944 16.701 616 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 2.60 % Allowed : 22.51 % Favored : 74.89 % 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: -4.19 (0.25), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 92 PHE 0.011 0.002 PHE E 101 TYR 0.018 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 151 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 0.620 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 141 average time/residue: 0.2846 time to fit residues: 52.9634 Evaluate side-chains 141 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 0.668 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.1058 time to fit residues: 2.4522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 44 optimal weight: 0.0060 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: 0.8998 ------------------------------------------------------------------------------- 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: 0.8107 moved from start: 0.5890 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= 0.224 Angle : 0.583 4.268 5929 Z= 0.307 Chirality : 0.043 0.133 693 Planarity : 0.003 0.028 749 Dihedral : 5.923 16.135 616 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.52 % Allowed : 24.03 % Favored : 74.46 % 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 (0.25), 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 0.003 0.001 TRP G 92 PHE 0.007 0.001 PHE G 101 TYR 0.015 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 142 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 135 time to evaluate : 0.656 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 135 average time/residue: 0.2760 time to fit residues: 48.5826 Evaluate side-chains 136 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 0.656 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.0980 time to fit residues: 1.6233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.8127 moved from start: 0.6076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4347 Z= 0.281 Angle : 0.604 4.354 5929 Z= 0.318 Chirality : 0.044 0.135 693 Planarity : 0.003 0.027 749 Dihedral : 5.894 14.845 616 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 1.95 % Allowed : 24.89 % 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: -4.22 (0.24), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 92 PHE 0.008 0.001 PHE G 101 TYR 0.015 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 135 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 126 time to evaluate : 0.658 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 128 average time/residue: 0.2818 time to fit residues: 46.9637 Evaluate side-chains 130 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 125 time to evaluate : 0.682 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.0992 time to fit residues: 1.6597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8109 moved from start: 0.6174 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= 0.187 Angle : 0.577 4.280 5929 Z= 0.301 Chirality : 0.043 0.137 693 Planarity : 0.003 0.027 749 Dihedral : 5.812 14.300 616 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.08 % Allowed : 25.54 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.25), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (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 G 101 TYR 0.014 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 137 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 132 time to evaluate : 0.557 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 132 average time/residue: 0.2720 time to fit residues: 46.7721 Evaluate side-chains 131 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 126 time to evaluate : 0.661 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1028 time to fit residues: 1.5804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.0040 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 0.0050 chunk 44 optimal weight: 1.9990 overall best weight: 0.6808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** 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 0.022 4347 Z= 0.194 Angle : 0.570 4.170 5929 Z= 0.299 Chirality : 0.043 0.134 693 Planarity : 0.003 0.026 749 Dihedral : 5.733 14.354 616 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.87 % Allowed : 26.19 % Favored : 72.94 % 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 : -3.15 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP G 92 PHE 0.005 0.001 PHE G 101 TYR 0.015 0.001 TYR E 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 131 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 0.629 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 128 average time/residue: 0.2817 time to fit residues: 47.0227 Evaluate side-chains 129 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 0.684 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1107 time to fit residues: 1.2893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 35 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 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: 0.8113 moved from start: 0.6338 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= 0.217 Angle : 0.582 4.133 5929 Z= 0.304 Chirality : 0.044 0.133 693 Planarity : 0.003 0.028 749 Dihedral : 5.707 14.537 616 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.65 % Allowed : 26.41 % Favored : 72.94 % 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: -4.13 (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 0.003 0.001 TRP G 92 PHE 0.005 0.001 PHE G 101 TYR 0.017 0.002 TYR D 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 132 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 129 average time/residue: 0.3051 time to fit residues: 51.3044 Evaluate side-chains 132 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 0.657 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1199 time to fit residues: 1.3473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 50 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 35 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.126583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.111961 restraints weight = 17947.520| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.74 r_work: 0.3728 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.6414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4347 Z= 0.161 Angle : 0.557 4.354 5929 Z= 0.291 Chirality : 0.043 0.133 693 Planarity : 0.003 0.027 749 Dihedral : 5.615 14.037 616 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.87 % Allowed : 25.76 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 0.000 TRP A 92 PHE 0.006 0.001 PHE G 101 TYR 0.014 0.001 TYR D 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3306.25 seconds wall clock time: 58 minutes 46.89 seconds (3526.89 seconds total)