Starting phenix.real_space_refine on Thu Feb 15 19:26:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk4_25172/02_2024/7sk4_25172_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk4_25172/02_2024/7sk4_25172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk4_25172/02_2024/7sk4_25172.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk4_25172/02_2024/7sk4_25172.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk4_25172/02_2024/7sk4_25172_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk4_25172/02_2024/7sk4_25172_trim_updated.pdb" } resolution = 3.3 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= -0.001 sd= 0.037 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 37 5.16 5 C 4330 2.51 5 N 1084 2.21 5 O 1205 1.98 5 H 6489 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13145 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 4995 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 11, 'TRANS': 293} Chain: "B" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1171 Classifications: {'peptide': 69} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "C" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1615 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1913 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "E" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1533 Classifications: {'peptide': 101} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "F" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1862 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.35, per 1000 atoms: 0.48 Number of scatterers: 13145 At special positions: 0 Unit cell: (66.96, 77.76, 149.04, 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 37 16.00 O 1205 8.00 N 1084 7.00 C 4330 6.00 H 6489 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 34 " distance=2.03 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 50 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.04 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.04 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.50 Conformation dependent library (CDL) restraints added in 1.4 seconds 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1570 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 11 sheets defined 30.3% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 40 through 75 removed outlier: 3.808A pdb=" N PHE A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR A 75 " --> pdb=" O GLN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 105 removed outlier: 3.916A pdb=" N ILE A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Proline residue: A 98 - end of helix Processing helix chain 'A' and resid 114 through 147 removed outlier: 3.924A pdb=" N TYR A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 154 through 181 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 205 through 217 Processing helix chain 'A' and resid 222 through 241 removed outlier: 3.638A pdb=" N LEU A 235 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 248 No H-bonds generated for 'chain 'A' and resid 245 through 248' Processing helix chain 'A' and resid 252 through 279 Proline residue: A 267 - end of helix Processing helix chain 'A' and resid 287 through 315 removed outlier: 3.844A pdb=" N HIS A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N CYS A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N CYS A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Proline residue: A 312 - end of helix Processing helix chain 'A' and resid 320 through 330 Processing helix chain 'B' and resid 3 through 5 No H-bonds generated for 'chain 'B' and resid 3 through 5' Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 56 through 67 Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing sheet with id= A, first strand: chain 'A' and resid 183 through 187 Processing sheet with id= B, first strand: chain 'B' and resid 27 through 31 Processing sheet with id= C, first strand: chain 'C' and resid 5 through 8 Processing sheet with id= D, first strand: chain 'C' and resid 11 through 13 removed outlier: 5.576A pdb=" N LYS C 104 " --> pdb=" O LEU C 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 34 through 39 Processing sheet with id= F, first strand: chain 'D' and resid 6 through 10 removed outlier: 3.549A pdb=" N MET D 86 " --> pdb=" O LEU D 21 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 122 through 124 removed outlier: 5.921A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA D 43 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU D 48 " --> pdb=" O ALA D 43 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 5 through 8 Processing sheet with id= I, first strand: chain 'F' and resid 6 through 10 Processing sheet with id= J, first strand: chain 'F' and resid 124 through 126 removed outlier: 3.744A pdb=" N ALA F 52 " --> pdb=" O TRP F 39 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ARG F 41 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TRP F 50 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA F 43 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU F 48 " --> pdb=" O ALA F 43 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 100 through 102 removed outlier: 3.962A pdb=" N TYR F 119 " --> pdb=" O ARG F 101 " (cutoff:3.500A) 279 hydrogen bonds defined for protein. 792 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: 4.48 Time building geometry restraints manager: 10.89 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: 6479 1.03 - 1.23: 13 1.23 - 1.42: 2994 1.42 - 1.62: 3796 1.62 - 1.81: 50 Bond restraints: 13332 Sorted by residual: bond pdb=" C6 CLR A 401 " pdb=" C7 CLR A 401 " ideal model delta sigma weight residual 1.492 1.539 -0.047 2.00e-02 2.50e+03 5.53e+00 bond pdb=" C6 CLR A 402 " pdb=" C7 CLR A 402 " ideal model delta sigma weight residual 1.492 1.539 -0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" C20 CLR A 402 " pdb=" C22 CLR A 402 " ideal model delta sigma weight residual 1.535 1.576 -0.041 2.00e-02 2.50e+03 4.17e+00 bond pdb=" C13 CLR A 401 " pdb=" C14 CLR A 401 " ideal model delta sigma weight residual 1.537 1.578 -0.041 2.00e-02 2.50e+03 4.11e+00 bond pdb=" C13 CLR A 402 " pdb=" C14 CLR A 402 " ideal model delta sigma weight residual 1.537 1.577 -0.040 2.00e-02 2.50e+03 4.03e+00 ... (remaining 13327 not shown) Histogram of bond angle deviations from ideal: 97.89 - 105.10: 106 105.10 - 112.32: 14922 112.32 - 119.53: 3210 119.53 - 126.75: 5574 126.75 - 133.96: 128 Bond angle restraints: 23940 Sorted by residual: angle pdb=" C22 CLR A 401 " pdb=" C23 CLR A 401 " pdb=" C24 CLR A 401 " ideal model delta sigma weight residual 111.95 103.86 8.09 3.00e+00 1.11e-01 7.28e+00 angle pdb=" C22 CLR A 402 " pdb=" C23 CLR A 402 " pdb=" C24 CLR A 402 " ideal model delta sigma weight residual 111.95 104.04 7.91 3.00e+00 1.11e-01 6.95e+00 angle pdb=" C23 CLR A 402 " pdb=" C24 CLR A 402 " pdb=" C25 CLR A 402 " ideal model delta sigma weight residual 115.14 108.71 6.43 3.00e+00 1.11e-01 4.59e+00 angle pdb=" C23 CLR A 401 " pdb=" C24 CLR A 401 " pdb=" C25 CLR A 401 " ideal model delta sigma weight residual 115.14 109.01 6.13 3.00e+00 1.11e-01 4.17e+00 angle pdb=" C17 CLR A 401 " pdb=" C20 CLR A 401 " pdb=" C22 CLR A 401 " ideal model delta sigma weight residual 109.45 103.60 5.85 3.00e+00 1.11e-01 3.81e+00 ... (remaining 23935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 5892 17.74 - 35.48: 449 35.48 - 53.22: 111 53.22 - 70.96: 29 70.96 - 88.70: 7 Dihedral angle restraints: 6488 sinusoidal: 3434 harmonic: 3054 Sorted by residual: dihedral pdb=" CB CYS F 25 " pdb=" SG CYS F 25 " pdb=" SG CYS F 99 " pdb=" CB CYS F 99 " ideal model delta sinusoidal sigma weight residual 93.00 61.76 31.24 1 1.00e+01 1.00e-02 1.39e+01 dihedral pdb=" CA THR A 147 " pdb=" C THR A 147 " pdb=" N TYR A 148 " pdb=" CA TYR A 148 " ideal model delta harmonic sigma weight residual -180.00 -164.02 -15.98 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA PRO A 38 " pdb=" C PRO A 38 " pdb=" N ASN A 39 " pdb=" CA ASN A 39 " ideal model delta harmonic sigma weight residual 180.00 -164.63 -15.37 0 5.00e+00 4.00e-02 9.45e+00 ... (remaining 6485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 954 0.071 - 0.142: 86 0.142 - 0.212: 1 0.212 - 0.283: 2 0.283 - 0.354: 6 Chirality restraints: 1049 Sorted by residual: chirality pdb=" C17 CLR A 401 " pdb=" C13 CLR A 401 " pdb=" C16 CLR A 401 " pdb=" C20 CLR A 401 " both_signs ideal model delta sigma weight residual False 2.55 2.91 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" C17 CLR A 402 " pdb=" C13 CLR A 402 " pdb=" C16 CLR A 402 " pdb=" C20 CLR A 402 " both_signs ideal model delta sigma weight residual False 2.55 2.90 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C20 CLR A 401 " pdb=" C17 CLR A 401 " pdb=" C21 CLR A 401 " pdb=" C22 CLR A 401 " both_signs ideal model delta sigma weight residual False 2.59 2.91 -0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 1046 not shown) Planarity restraints: 1926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 40 " -0.017 5.00e-02 4.00e+02 2.52e-02 1.01e+00 pdb=" N PRO C 41 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 41 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 41 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 34 " 0.016 5.00e-02 4.00e+02 2.40e-02 9.23e-01 pdb=" N PRO A 35 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 35 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 35 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 272 " 0.005 2.00e-02 2.50e+03 9.22e-03 8.50e-01 pdb=" C VAL A 272 " -0.016 2.00e-02 2.50e+03 pdb=" O VAL A 272 " 0.006 2.00e-02 2.50e+03 pdb=" N LEU A 273 " 0.005 2.00e-02 2.50e+03 ... (remaining 1923 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 605 2.19 - 2.79: 26133 2.79 - 3.39: 35342 3.39 - 4.00: 46689 4.00 - 4.60: 72190 Nonbonded interactions: 180959 Sorted by model distance: nonbonded pdb=" OE1 GLU C 82 " pdb=" H GLU C 82 " model vdw 1.585 1.850 nonbonded pdb=" O VAL A 217 " pdb=" H PHE A 221 " model vdw 1.602 1.850 nonbonded pdb="HH22 ARG D 70 " pdb=" OD1 ASP D 93 " model vdw 1.613 1.850 nonbonded pdb=" H ARG D 90 " pdb=" OD2 ASP D 93 " model vdw 1.666 1.850 nonbonded pdb=" O ILE A 123 " pdb="HD22 ASN A 127 " model vdw 1.668 1.850 ... (remaining 180954 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 'C' and (resid 3 through 13 or resid 18 through 91 or resid 93 through 94 \ or resid 98 through 106)) selection = (chain 'E' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG \ 13 or name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13 \ )) or resid 4 through 91 or resid 93 through 94 or resid 98 through 106)) } ncs_group { reference = (chain 'D' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2)) or resid 6 through 31 or resid 33 or resid 35 through 5 \ 2 or resid 54 or resid 57 through 88 or (resid 89 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name HB \ 2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or \ name HD22 or name HD23)) or resid 90 through 102 or resid 105 through 106 or res \ id 111 or resid 113 or resid 116 through 127)) selection = (chain 'F' and (resid 5 through 31 or resid 33 or resid 35 through 52 or resid 5 \ 4 or resid 57 through 102 or resid 105 or resid 109 or resid 114 or resid 116 or \ resid 118 through 129)) } 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: 2.650 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: 0.200 Extract box with map and model: 13.870 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 45.300 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 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 : 0.003 0.047 6843 Z= 0.209 Angle : 0.503 8.094 9329 Z= 0.241 Chirality : 0.048 0.354 1049 Planarity : 0.002 0.025 1135 Dihedral : 14.269 88.702 2499 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.30), residues: 817 helix: 2.23 (0.33), residues: 246 sheet: -0.92 (0.34), residues: 236 loop : -1.44 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 109 HIS 0.002 0.001 HIS B 2 PHE 0.007 0.001 PHE F 30 TYR 0.010 0.001 TYR E 50 ARG 0.005 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7580 (t80) cc_final: 0.7217 (t80) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.4274 time to fit residues: 54.2452 Evaluate side-chains 77 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 62 optimal weight: 0.2980 chunk 24 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.0637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6843 Z= 0.181 Angle : 0.475 4.121 9329 Z= 0.253 Chirality : 0.040 0.156 1049 Planarity : 0.003 0.028 1135 Dihedral : 5.053 53.664 1048 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.41 % Allowed : 5.47 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.30), residues: 817 helix: 2.53 (0.32), residues: 244 sheet: -0.81 (0.34), residues: 236 loop : -1.45 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 107 HIS 0.003 0.001 HIS D 38 PHE 0.008 0.001 PHE A 124 TYR 0.012 0.001 TYR D 53 ARG 0.003 0.000 ARG F 101 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7586 (t80) cc_final: 0.7235 (t80) outliers start: 3 outliers final: 3 residues processed: 85 average time/residue: 0.4162 time to fit residues: 47.3285 Evaluate side-chains 80 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain E residue 61 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 24 optimal weight: 0.0070 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- 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: 0.8003 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6843 Z= 0.198 Angle : 0.467 4.344 9329 Z= 0.250 Chirality : 0.040 0.153 1049 Planarity : 0.003 0.029 1135 Dihedral : 4.923 50.807 1048 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.96 % Allowed : 5.88 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.30), residues: 817 helix: 2.59 (0.32), residues: 245 sheet: -0.80 (0.34), residues: 236 loop : -1.48 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 265 HIS 0.003 0.001 HIS D 38 PHE 0.008 0.001 PHE A 124 TYR 0.010 0.001 TYR C 92 ARG 0.003 0.000 ARG B 1 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7541 (t80) cc_final: 0.7209 (t80) outliers start: 7 outliers final: 6 residues processed: 88 average time/residue: 0.4369 time to fit residues: 50.6707 Evaluate side-chains 87 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 61 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 73 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 64 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7992 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6843 Z= 0.168 Angle : 0.455 4.264 9329 Z= 0.241 Chirality : 0.039 0.152 1049 Planarity : 0.003 0.029 1135 Dihedral : 4.729 47.376 1048 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.55 % Allowed : 8.34 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.30), residues: 817 helix: 2.74 (0.32), residues: 245 sheet: -0.76 (0.34), residues: 234 loop : -1.46 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 265 HIS 0.003 0.001 HIS A 298 PHE 0.008 0.001 PHE A 124 TYR 0.008 0.001 TYR C 92 ARG 0.002 0.000 ARG F 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7516 (t80) cc_final: 0.7199 (t80) REVERT: D 79 LYS cc_start: 0.6743 (mtmm) cc_final: 0.6509 (mtmm) outliers start: 4 outliers final: 4 residues processed: 89 average time/residue: 0.4375 time to fit residues: 51.6359 Evaluate side-chains 87 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain E residue 61 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6843 Z= 0.213 Angle : 0.476 4.516 9329 Z= 0.253 Chirality : 0.040 0.150 1049 Planarity : 0.003 0.030 1135 Dihedral : 4.691 43.282 1048 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.09 % Allowed : 8.89 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.30), residues: 817 helix: 2.67 (0.32), residues: 246 sheet: -0.80 (0.34), residues: 234 loop : -1.52 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 265 HIS 0.003 0.001 HIS D 38 PHE 0.008 0.001 PHE A 124 TYR 0.010 0.001 TYR C 92 ARG 0.003 0.000 ARG B 1 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7503 (t80) cc_final: 0.7201 (t80) REVERT: D 79 LYS cc_start: 0.6834 (mtmm) cc_final: 0.6605 (mtmm) outliers start: 8 outliers final: 7 residues processed: 85 average time/residue: 0.4010 time to fit residues: 45.9262 Evaluate side-chains 86 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain D residue 53 TYR Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 61 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6843 Z= 0.225 Angle : 0.482 4.616 9329 Z= 0.257 Chirality : 0.040 0.150 1049 Planarity : 0.003 0.030 1135 Dihedral : 4.634 37.681 1048 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.09 % Allowed : 9.17 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.30), residues: 817 helix: 2.65 (0.32), residues: 246 sheet: -0.79 (0.34), residues: 234 loop : -1.54 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 265 HIS 0.004 0.001 HIS D 38 PHE 0.009 0.001 PHE A 124 TYR 0.010 0.001 TYR A 322 ARG 0.003 0.000 ARG B 1 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7529 (t80) cc_final: 0.7226 (t80) outliers start: 8 outliers final: 7 residues processed: 86 average time/residue: 0.4435 time to fit residues: 51.1527 Evaluate side-chains 88 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain D residue 53 TYR Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 61 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7997 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6843 Z= 0.167 Angle : 0.459 4.601 9329 Z= 0.243 Chirality : 0.040 0.151 1049 Planarity : 0.003 0.030 1135 Dihedral : 4.429 33.393 1048 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.96 % Allowed : 9.58 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.30), residues: 817 helix: 2.77 (0.32), residues: 246 sheet: -0.70 (0.35), residues: 234 loop : -1.48 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 265 HIS 0.003 0.001 HIS D 38 PHE 0.008 0.001 PHE A 124 TYR 0.008 0.001 TYR C 92 ARG 0.004 0.000 ARG B 1 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7504 (t80) cc_final: 0.7209 (t80) outliers start: 7 outliers final: 6 residues processed: 86 average time/residue: 0.3852 time to fit residues: 45.5874 Evaluate side-chains 86 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 61 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 7 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.8023 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6843 Z= 0.236 Angle : 0.489 4.686 9329 Z= 0.261 Chirality : 0.040 0.150 1049 Planarity : 0.003 0.030 1135 Dihedral : 4.544 44.376 1048 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.09 % Allowed : 9.85 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.30), residues: 817 helix: 2.65 (0.32), residues: 246 sheet: -0.79 (0.34), residues: 234 loop : -1.61 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 50 HIS 0.004 0.001 HIS D 38 PHE 0.009 0.001 PHE A 124 TYR 0.011 0.001 TYR A 322 ARG 0.004 0.000 ARG B 1 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7530 (t80) cc_final: 0.7218 (t80) outliers start: 8 outliers final: 7 residues processed: 82 average time/residue: 0.3772 time to fit residues: 42.7260 Evaluate side-chains 84 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain D residue 53 TYR Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 61 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 46 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: 0.8011 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6843 Z= 0.195 Angle : 0.477 4.575 9329 Z= 0.253 Chirality : 0.040 0.151 1049 Planarity : 0.003 0.030 1135 Dihedral : 4.525 52.261 1048 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.82 % Allowed : 10.67 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.30), residues: 817 helix: 2.72 (0.32), residues: 246 sheet: -0.73 (0.35), residues: 234 loop : -1.56 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 109 HIS 0.003 0.001 HIS D 38 PHE 0.008 0.001 PHE A 124 TYR 0.009 0.001 TYR C 92 ARG 0.004 0.000 ARG B 1 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7498 (t80) cc_final: 0.7192 (t80) outliers start: 6 outliers final: 6 residues processed: 83 average time/residue: 0.3767 time to fit residues: 42.6743 Evaluate side-chains 84 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain D residue 53 TYR Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 61 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 0.0770 chunk 6 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- 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: 0.8022 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6843 Z= 0.228 Angle : 0.497 6.322 9329 Z= 0.263 Chirality : 0.040 0.150 1049 Planarity : 0.003 0.031 1135 Dihedral : 4.612 55.372 1048 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.82 % Allowed : 10.81 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.30), residues: 817 helix: 2.65 (0.32), residues: 246 sheet: -0.79 (0.35), residues: 234 loop : -1.64 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 109 HIS 0.004 0.001 HIS D 38 PHE 0.009 0.001 PHE A 124 TYR 0.011 0.001 TYR A 322 ARG 0.004 0.000 ARG B 1 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7512 (t80) cc_final: 0.7204 (t80) outliers start: 6 outliers final: 6 residues processed: 84 average time/residue: 0.4198 time to fit residues: 48.3998 Evaluate side-chains 83 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain D residue 53 TYR Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 61 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.091914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.084061 restraints weight = 48560.876| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.42 r_work: 0.3378 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6843 Z= 0.220 Angle : 0.494 5.693 9329 Z= 0.261 Chirality : 0.040 0.151 1049 Planarity : 0.003 0.030 1135 Dihedral : 4.655 58.926 1048 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.82 % Allowed : 10.94 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.30), residues: 817 helix: 2.65 (0.32), residues: 246 sheet: -0.78 (0.35), residues: 229 loop : -1.64 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 109 HIS 0.004 0.001 HIS D 38 PHE 0.008 0.001 PHE A 124 TYR 0.010 0.001 TYR A 322 ARG 0.004 0.000 ARG B 1 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3677.36 seconds wall clock time: 65 minutes 45.72 seconds (3945.72 seconds total)