Starting phenix.real_space_refine (version: dev) on Mon Feb 20 22:29:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk4_25172/02_2023/7sk4_25172_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk4_25172/02_2023/7sk4_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_2023/7sk4_25172.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk4_25172/02_2023/7sk4_25172.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk4_25172/02_2023/7sk4_25172_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk4_25172/02_2023/7sk4_25172_trim_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 6.39, per 1000 atoms: 0.49 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: 9.96 Conformation dependent library (CDL) restraints added in 1.2 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: 0.70 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: 4.89 Time building geometry restraints manager: 10.46 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: 4992 17.74 - 35.48: 402 35.48 - 53.22: 63 53.22 - 70.96: 12 70.96 - 88.70: 7 Dihedral angle restraints: 5476 sinusoidal: 2422 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 5473 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 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. 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: 2.570 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: 15.010 Check model and map are aligned: 0.180 Process input model: 43.070 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.110 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 14.475 88.702 2387 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 % 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 *********************** 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 : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.4341 time to fit residues: 55.1605 Evaluate side-chains 77 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.084 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2383 ------------------------------------------------------------------------------- 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: 0.6980 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7959 moved from start: 0.0633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 6843 Z= 0.198 Angle : 0.479 4.300 9329 Z= 0.255 Chirality : 0.040 0.153 1049 Planarity : 0.003 0.027 1135 Dihedral : 4.637 54.168 936 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer Outliers : 0.55 % 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: -0.14 (0.30), residues: 817 helix: 2.45 (0.32), residues: 245 sheet: -0.85 (0.34), residues: 236 loop : -1.46 (0.33), residues: 336 *********************** 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 85 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 83 average time/residue: 0.4113 time to fit residues: 45.6138 Evaluate side-chains 80 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 1.168 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1603 time to fit residues: 2.2369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- 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: 0.7971 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 6843 Z= 0.234 Angle : 0.490 4.750 9329 Z= 0.262 Chirality : 0.040 0.153 1049 Planarity : 0.003 0.028 1135 Dihedral : 4.661 50.340 936 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 0.68 % 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: -0.17 (0.30), residues: 817 helix: 2.51 (0.32), residues: 245 sheet: -0.88 (0.34), residues: 236 loop : -1.54 (0.33), residues: 336 *********************** 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 89 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 88 average time/residue: 0.4418 time to fit residues: 51.1589 Evaluate side-chains 83 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 1.085 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1521 time to fit residues: 2.5069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 6843 Z= 0.269 Angle : 0.507 5.216 9329 Z= 0.273 Chirality : 0.040 0.153 1049 Planarity : 0.003 0.028 1135 Dihedral : 4.756 47.644 936 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer Outliers : 0.14 % 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: -0.33 (0.30), residues: 817 helix: 2.41 (0.32), residues: 246 sheet: -1.00 (0.34), residues: 231 loop : -1.65 (0.32), residues: 340 *********************** 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 83 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 83 average time/residue: 0.4462 time to fit residues: 49.0997 Evaluate side-chains 78 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 1.113 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1819 time to fit residues: 1.6417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 31 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.7987 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 6843 Z= 0.250 Angle : 0.507 5.176 9329 Z= 0.271 Chirality : 0.040 0.151 1049 Planarity : 0.003 0.029 1135 Dihedral : 4.737 44.937 936 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer Outliers : 0.41 % 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: -0.33 (0.30), residues: 817 helix: 2.42 (0.32), residues: 246 sheet: -0.98 (0.34), residues: 229 loop : -1.68 (0.32), residues: 342 *********************** 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 83 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 81 average time/residue: 0.4264 time to fit residues: 46.0327 Evaluate side-chains 80 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 1.069 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1468 time to fit residues: 1.8527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 45 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 74 optimal weight: 0.0980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 HIS ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1086 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= 0.201 Angle : 0.488 4.972 9329 Z= 0.258 Chirality : 0.040 0.152 1049 Planarity : 0.003 0.028 1135 Dihedral : 4.623 42.755 936 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer Outliers : 0.14 % 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: -0.15 (0.30), residues: 817 helix: 2.56 (0.32), residues: 246 sheet: -0.84 (0.34), residues: 234 loop : -1.58 (0.33), residues: 337 *********************** 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 82 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 82 average time/residue: 0.4163 time to fit residues: 46.0026 Evaluate side-chains 81 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1976 time to fit residues: 1.6603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.7967 moved from start: 0.1126 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= 0.191 Angle : 0.478 4.892 9329 Z= 0.253 Chirality : 0.040 0.150 1049 Planarity : 0.003 0.028 1135 Dihedral : 4.543 40.211 936 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 0.14 % 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: 2.63 (0.32), residues: 246 sheet: -0.80 (0.34), residues: 234 loop : -1.57 (0.33), residues: 337 *********************** 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 84 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 83 average time/residue: 0.4079 time to fit residues: 45.7467 Evaluate side-chains 81 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 1.034 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1730 time to fit residues: 1.9561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0980 chunk 14 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1193 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= 0.232 Angle : 0.498 5.135 9329 Z= 0.265 Chirality : 0.040 0.149 1049 Planarity : 0.003 0.029 1135 Dihedral : 4.615 37.922 936 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer Outliers : 0.41 % 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: -0.22 (0.30), residues: 817 helix: 2.60 (0.32), residues: 245 sheet: -0.92 (0.35), residues: 229 loop : -1.66 (0.32), residues: 343 *********************** 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 81 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 80 average time/residue: 0.3862 time to fit residues: 42.1790 Evaluate side-chains 80 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 1.124 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1591 time to fit residues: 2.1197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 64 optimal weight: 0.3980 chunk 67 optimal weight: 0.8980 chunk 47 optimal weight: 0.0980 chunk 75 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7960 moved from start: 0.1182 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= 0.175 Angle : 0.475 4.780 9329 Z= 0.252 Chirality : 0.040 0.150 1049 Planarity : 0.003 0.028 1135 Dihedral : 4.479 36.262 936 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 0.00 % 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: -0.02 (0.30), residues: 817 helix: 2.75 (0.32), residues: 245 sheet: -0.76 (0.35), residues: 229 loop : -1.57 (0.32), residues: 343 *********************** 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 82 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.3951 time to fit residues: 44.4222 Evaluate side-chains 79 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.201 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 73 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 67 optimal weight: 0.0000 chunk 19 optimal weight: 0.5980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1230 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= 0.173 Angle : 0.470 4.719 9329 Z= 0.249 Chirality : 0.040 0.148 1049 Planarity : 0.003 0.028 1135 Dihedral : 4.392 33.273 936 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer Outliers : 0.14 % 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: 2.85 (0.32), residues: 245 sheet: -0.70 (0.35), residues: 234 loop : -1.54 (0.33), residues: 338 ********************** 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 81 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 81 average time/residue: 0.4618 time to fit residues: 49.4732 Evaluate side-chains 79 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1894 time to fit residues: 1.6293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 17 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 65 optimal weight: 0.0770 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.092761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.084852 restraints weight = 48141.648| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.44 r_work: 0.3391 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1230 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= 0.187 Angle : 0.487 6.885 9329 Z= 0.255 Chirality : 0.040 0.148 1049 Planarity : 0.003 0.028 1135 Dihedral : 4.393 31.782 936 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer Outliers : 0.00 % 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: 0.05 (0.30), residues: 817 helix: 2.84 (0.32), residues: 245 sheet: -0.72 (0.35), residues: 229 loop : -1.56 (0.32), residues: 343 =============================================================================== Job complete usr+sys time: 3605.35 seconds wall clock time: 64 minutes 13.48 seconds (3853.48 seconds total)