Starting phenix.real_space_refine on Sun Mar 10 18:18:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaf_36126/03_2024/8jaf_36126_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaf_36126/03_2024/8jaf_36126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaf_36126/03_2024/8jaf_36126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaf_36126/03_2024/8jaf_36126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaf_36126/03_2024/8jaf_36126_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaf_36126/03_2024/8jaf_36126_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 P 4 5.49 5 S 12 5.16 5 C 2464 2.51 5 N 658 2.21 5 O 724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3862 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2253 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 292} Chain breaks: 7 Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 365 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 166 Chain: "H" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 832 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "L" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 716 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ARG:plan': 3, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 2.65, per 1000 atoms: 0.69 Number of scatterers: 3862 At special positions: 0 Unit cell: (68.89, 83.83, 95.45, 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 12 16.00 P 4 15.00 O 724 8.00 N 658 7.00 C 2464 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 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: 1.53 Conformation dependent library (CDL) restraints added in 828.6 milliseconds 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1032 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 7 helices and 13 sheets defined 5.5% alpha, 36.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 99 through 107 removed outlier: 3.918A pdb=" N ARG A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 removed outlier: 5.646A pdb=" N GLU A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'H' and resid 56 through 58 No H-bonds generated for 'chain 'H' and resid 56 through 58' Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing sheet with id= A, first strand: chain 'A' and resid 19 through 22 removed outlier: 3.694A pdb=" N THR A 19 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 40 " --> pdb=" O TYR A 21 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.618A pdb=" N ARG A 169 " --> pdb=" O PHE A 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 164 through 168 removed outlier: 3.670A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE A 61 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ASP A 78 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N TYR A 63 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ARG A 76 " --> pdb=" O TYR A 63 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 127 through 129 Processing sheet with id= E, first strand: chain 'A' and resid 184 through 188 removed outlier: 3.523A pdb=" N ALA A 201 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 274 " --> pdb=" O ILE A 214 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 207 through 209 removed outlier: 5.981A pdb=" N THR A 350 " --> pdb=" O TYR A 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 342 through 349 removed outlier: 6.242A pdb=" N GLN A 237 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ALA A 239 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LYS A 250 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE A 241 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLN A 248 " --> pdb=" O ILE A 241 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.508A pdb=" N LEU H 21 " --> pdb=" O MET H 86 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU H 23 " --> pdb=" O LEU H 84 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 117 through 119 removed outlier: 3.675A pdb=" N VAL H 96 " --> pdb=" O GLN H 42 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ALA H 43 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU H 48 " --> pdb=" O ALA H 43 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 100 through 102 removed outlier: 3.580A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'L' and resid 6 through 8 removed outlier: 3.548A pdb=" N SER L 8 " --> pdb=" O THR L 23 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR L 23 " --> pdb=" O SER L 8 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.366A pdb=" N LYS L 104 " --> pdb=" O LEU L 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'L' and resid 86 through 91 removed outlier: 3.706A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) 120 hydrogen bonds defined for protein. 321 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: 1.06 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1224 1.34 - 1.46: 729 1.46 - 1.57: 1964 1.57 - 1.69: 14 1.69 - 1.81: 15 Bond restraints: 3946 Sorted by residual: bond pdb=" OG1 TPO V 307 " pdb=" P TPO V 307 " ideal model delta sigma weight residual 1.717 1.605 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" OG1 TPO V 310 " pdb=" P TPO V 310 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" O3P TPO V 310 " pdb=" P TPO V 310 " ideal model delta sigma weight residual 1.528 1.607 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" O2P TPO V 310 " pdb=" P TPO V 310 " ideal model delta sigma weight residual 1.528 1.606 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" O2P TPO V 307 " pdb=" P TPO V 307 " ideal model delta sigma weight residual 1.528 1.606 -0.078 2.00e-02 2.50e+03 1.50e+01 ... (remaining 3941 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.17: 147 106.17 - 113.14: 2162 113.14 - 120.12: 1256 120.12 - 127.09: 1794 127.09 - 134.06: 55 Bond angle restraints: 5414 Sorted by residual: angle pdb=" N HIS A 30 " pdb=" CA HIS A 30 " pdb=" C HIS A 30 " ideal model delta sigma weight residual 112.72 105.48 7.24 1.36e+00 5.41e-01 2.83e+01 angle pdb=" N ARG A 161 " pdb=" CA ARG A 161 " pdb=" C ARG A 161 " ideal model delta sigma weight residual 107.48 119.46 -11.98 2.29e+00 1.91e-01 2.74e+01 angle pdb=" C HIS A 30 " pdb=" CA HIS A 30 " pdb=" CB HIS A 30 " ideal model delta sigma weight residual 111.22 116.16 -4.94 1.23e+00 6.61e-01 1.61e+01 angle pdb=" N ASN A 162 " pdb=" CA ASN A 162 " pdb=" CB ASN A 162 " ideal model delta sigma weight residual 110.49 117.07 -6.58 1.69e+00 3.50e-01 1.51e+01 angle pdb=" OG1 TPO V 310 " pdb=" P TPO V 310 " pdb=" O1P TPO V 310 " ideal model delta sigma weight residual 100.43 111.27 -10.84 3.00e+00 1.11e-01 1.30e+01 ... (remaining 5409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.34: 2074 13.34 - 26.67: 180 26.67 - 40.01: 49 40.01 - 53.34: 16 53.34 - 66.68: 5 Dihedral angle restraints: 2324 sinusoidal: 731 harmonic: 1593 Sorted by residual: dihedral pdb=" CA THR L 70 " pdb=" C THR L 70 " pdb=" N ASP L 71 " pdb=" CA ASP L 71 " ideal model delta harmonic sigma weight residual 180.00 155.81 24.19 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA VAL A 235 " pdb=" C VAL A 235 " pdb=" N ARG A 236 " pdb=" CA ARG A 236 " ideal model delta harmonic sigma weight residual 180.00 -156.62 -23.38 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA TYR H 63 " pdb=" C TYR H 63 " pdb=" N ALA H 64 " pdb=" CA ALA H 64 " ideal model delta harmonic sigma weight residual -180.00 -157.08 -22.92 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 2321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 388 0.038 - 0.076: 151 0.076 - 0.113: 73 0.113 - 0.151: 25 0.151 - 0.189: 7 Chirality restraints: 644 Sorted by residual: chirality pdb=" CA LEU A 33 " pdb=" N LEU A 33 " pdb=" C LEU A 33 " pdb=" CB LEU A 33 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.93e-01 chirality pdb=" CA ARG A 161 " pdb=" N ARG A 161 " pdb=" C ARG A 161 " pdb=" CB ARG A 161 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.84e-01 chirality pdb=" CA GLU H 92 " pdb=" N GLU H 92 " pdb=" C GLU H 92 " pdb=" CB GLU H 92 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.42e-01 ... (remaining 641 not shown) Planarity restraints: 694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 181 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO A 182 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO A 182 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 182 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 29 " 0.020 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C ASP A 29 " -0.072 2.00e-02 2.50e+03 pdb=" O ASP A 29 " 0.027 2.00e-02 2.50e+03 pdb=" N HIS A 30 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 353 " 0.056 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO A 354 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 354 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 354 " 0.046 5.00e-02 4.00e+02 ... (remaining 691 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 706 2.77 - 3.30: 3781 3.30 - 3.83: 6306 3.83 - 4.37: 7133 4.37 - 4.90: 12695 Nonbonded interactions: 30621 Sorted by model distance: nonbonded pdb=" N ILE A 241 " pdb=" O ALA A 247 " model vdw 2.237 2.520 nonbonded pdb=" N TPO V 307 " pdb=" O1P TPO V 307 " model vdw 2.248 2.520 nonbonded pdb=" O PHE A 277 " pdb=" ND2 ASN A 281 " model vdw 2.277 2.520 nonbonded pdb=" O TYR A 321 " pdb=" O PHE A 349 " model vdw 2.279 3.040 nonbonded pdb=" NE ARG A 7 " pdb=" O2P SEP V 309 " model vdw 2.283 2.520 ... (remaining 30616 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.140 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.790 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5356 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 : 0.008 0.112 3946 Z= 0.487 Angle : 0.972 11.982 5414 Z= 0.525 Chirality : 0.054 0.189 644 Planarity : 0.008 0.104 694 Dihedral : 12.496 66.675 1286 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.87 % Allowed : 0.87 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.20 % 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: -2.04 (0.36), residues: 520 helix: -2.57 (1.26), residues: 14 sheet: -0.79 (0.34), residues: 234 loop : -1.79 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP H 113 HIS 0.007 0.002 HIS A 353 PHE 0.020 0.003 PHE A 27 TYR 0.024 0.003 TYR H 97 ARG 0.007 0.001 ARG H 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.442 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 0.1561 time to fit residues: 7.9922 Evaluate side-chains 34 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain H residue 92 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 27 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 0.2980 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 0.0980 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 0.0570 overall best weight: 0.2498 ------------------------------------------------------------------------------- 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: 0.5269 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3946 Z= 0.233 Angle : 0.666 5.567 5414 Z= 0.353 Chirality : 0.046 0.159 644 Planarity : 0.006 0.068 694 Dihedral : 7.290 47.297 590 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.45 % Allowed : 7.85 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.20 % 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: -1.72 (0.37), residues: 520 helix: -2.40 (1.03), residues: 14 sheet: -0.75 (0.35), residues: 227 loop : -1.37 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 113 HIS 0.006 0.001 HIS H 38 PHE 0.011 0.002 PHE A 115 TYR 0.015 0.002 TYR H 63 ARG 0.002 0.000 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.342 Fit side-chains REVERT: A 127 VAL cc_start: 0.7770 (t) cc_final: 0.7495 (p) REVERT: A 278 LEU cc_start: 0.4581 (tp) cc_final: 0.4335 (tp) outliers start: 5 outliers final: 2 residues processed: 37 average time/residue: 0.1295 time to fit residues: 6.5985 Evaluate side-chains 35 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain L residue 30 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 48 optimal weight: 0.0980 chunk 52 optimal weight: 0.5980 chunk 42 optimal weight: 0.0770 chunk 47 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5326 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3946 Z= 0.272 Angle : 0.646 5.806 5414 Z= 0.340 Chirality : 0.046 0.158 644 Planarity : 0.005 0.041 694 Dihedral : 6.291 46.396 583 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 1.74 % Allowed : 11.05 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.20 % 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: -1.43 (0.38), residues: 520 helix: 1.31 (1.63), residues: 7 sheet: -0.67 (0.35), residues: 230 loop : -1.20 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 36 HIS 0.006 0.001 HIS H 38 PHE 0.012 0.002 PHE A 268 TYR 0.024 0.002 TYR H 57 ARG 0.002 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.368 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 42 average time/residue: 0.1339 time to fit residues: 7.5966 Evaluate side-chains 39 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 30 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.0370 chunk 36 optimal weight: 0.0170 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 48 optimal weight: 0.0020 chunk 51 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 13 optimal weight: 0.0970 chunk 42 optimal weight: 0.0980 overall best weight: 0.0460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5158 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 3946 Z= 0.150 Angle : 0.553 5.796 5414 Z= 0.290 Chirality : 0.043 0.163 644 Planarity : 0.005 0.053 694 Dihedral : 5.515 45.574 583 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.29 % Allowed : 14.24 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.20 % 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: -1.20 (0.38), residues: 520 helix: -1.51 (1.36), residues: 14 sheet: -0.48 (0.35), residues: 229 loop : -0.97 (0.39), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 113 HIS 0.005 0.001 HIS H 38 PHE 0.010 0.001 PHE A 115 TYR 0.015 0.001 TYR A 272 ARG 0.002 0.000 ARG H 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.435 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 36 average time/residue: 0.1101 time to fit residues: 5.8332 Evaluate side-chains 32 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 chunk 21 optimal weight: 0.2980 chunk 43 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 26 optimal weight: 0.0170 chunk 45 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 46 optimal weight: 0.2980 overall best weight: 0.2618 ------------------------------------------------------------------------------- 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: 0.5266 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3946 Z= 0.216 Angle : 0.576 6.791 5414 Z= 0.299 Chirality : 0.044 0.146 644 Planarity : 0.005 0.056 694 Dihedral : 5.670 43.985 583 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.74 % Allowed : 15.12 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.20 % 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: -1.14 (0.38), residues: 520 helix: -1.29 (1.43), residues: 14 sheet: -0.52 (0.35), residues: 231 loop : -0.85 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 36 HIS 0.005 0.001 HIS H 38 PHE 0.010 0.001 PHE A 268 TYR 0.014 0.002 TYR A 272 ARG 0.002 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.413 Fit side-chains REVERT: L 71 ASP cc_start: 0.5087 (OUTLIER) cc_final: 0.4267 (t70) outliers start: 6 outliers final: 1 residues processed: 36 average time/residue: 0.1258 time to fit residues: 6.3349 Evaluate side-chains 32 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 71 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 0.0040 chunk 30 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 0.0970 chunk 26 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5308 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3946 Z= 0.253 Angle : 0.604 7.235 5414 Z= 0.314 Chirality : 0.044 0.160 644 Planarity : 0.005 0.057 694 Dihedral : 5.782 43.806 583 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.74 % Allowed : 16.28 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.20 % 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: -1.10 (0.38), residues: 520 helix: 1.97 (2.31), residues: 7 sheet: -0.60 (0.35), residues: 229 loop : -0.83 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 106 HIS 0.006 0.002 HIS A 219 PHE 0.010 0.002 PHE H 30 TYR 0.016 0.002 TYR A 21 ARG 0.002 0.000 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.429 Fit side-chains REVERT: L 71 ASP cc_start: 0.4986 (OUTLIER) cc_final: 0.4127 (t70) outliers start: 6 outliers final: 5 residues processed: 35 average time/residue: 0.1269 time to fit residues: 6.2337 Evaluate side-chains 37 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 71 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 31 optimal weight: 0.0170 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.0470 chunk 30 optimal weight: 0.4980 chunk 15 optimal weight: 0.2980 chunk 10 optimal weight: 0.0010 overall best weight: 0.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 42 GLN L 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5246 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3946 Z= 0.174 Angle : 0.549 7.026 5414 Z= 0.282 Chirality : 0.043 0.143 644 Planarity : 0.005 0.055 694 Dihedral : 5.437 46.193 583 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.74 % Allowed : 18.02 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.20 % 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: -1.01 (0.38), residues: 520 helix: 1.93 (2.35), residues: 7 sheet: -0.55 (0.35), residues: 229 loop : -0.76 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 106 HIS 0.005 0.001 HIS H 38 PHE 0.008 0.001 PHE A 115 TYR 0.018 0.001 TYR A 272 ARG 0.001 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.378 Fit side-chains REVERT: L 71 ASP cc_start: 0.4912 (OUTLIER) cc_final: 0.4117 (t70) outliers start: 6 outliers final: 4 residues processed: 36 average time/residue: 0.1027 time to fit residues: 5.5492 Evaluate side-chains 35 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 71 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 25 optimal weight: 0.0570 chunk 4 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 48 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 0.2980 chunk 28 optimal weight: 0.5980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5331 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3946 Z= 0.283 Angle : 0.634 7.650 5414 Z= 0.324 Chirality : 0.045 0.160 644 Planarity : 0.005 0.057 694 Dihedral : 5.781 43.698 583 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.62 % Allowed : 17.44 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.20 % 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: -1.20 (0.38), residues: 520 helix: 0.95 (1.89), residues: 10 sheet: -0.67 (0.35), residues: 228 loop : -0.89 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 106 HIS 0.006 0.002 HIS A 219 PHE 0.010 0.002 PHE H 30 TYR 0.013 0.002 TYR H 63 ARG 0.003 0.000 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.405 Fit side-chains REVERT: L 71 ASP cc_start: 0.5170 (OUTLIER) cc_final: 0.4412 (t70) outliers start: 9 outliers final: 8 residues processed: 42 average time/residue: 0.1298 time to fit residues: 7.4355 Evaluate side-chains 42 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 71 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 50 optimal weight: 0.1980 chunk 30 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 42 GLN H 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5385 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3946 Z= 0.335 Angle : 0.673 8.777 5414 Z= 0.343 Chirality : 0.046 0.156 644 Planarity : 0.006 0.060 694 Dihedral : 6.059 42.014 583 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.20 % Allowed : 16.86 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.20 % 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: -1.64 (0.37), residues: 520 helix: -1.25 (1.33), residues: 16 sheet: -0.84 (0.36), residues: 220 loop : -1.23 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 106 HIS 0.007 0.002 HIS A 219 PHE 0.014 0.002 PHE H 30 TYR 0.015 0.002 TYR H 63 ARG 0.003 0.001 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 31 time to evaluate : 0.363 Fit side-chains outliers start: 11 outliers final: 11 residues processed: 40 average time/residue: 0.1218 time to fit residues: 6.7364 Evaluate side-chains 43 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 32 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 71 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.0980 chunk 48 optimal weight: 0.7980 chunk 42 optimal weight: 0.1980 chunk 4 optimal weight: 0.4980 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 chunk 33 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5342 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3946 Z= 0.249 Angle : 0.625 7.766 5414 Z= 0.320 Chirality : 0.045 0.173 644 Planarity : 0.005 0.060 694 Dihedral : 5.792 44.153 583 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.33 % Allowed : 17.44 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.20 % 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: -1.51 (0.38), residues: 520 helix: -1.12 (1.30), residues: 16 sheet: -0.79 (0.35), residues: 228 loop : -1.11 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 106 HIS 0.005 0.001 HIS A 219 PHE 0.011 0.001 PHE H 30 TYR 0.012 0.002 TYR A 272 ARG 0.002 0.000 ARG A 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.389 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 40 average time/residue: 0.1288 time to fit residues: 7.1401 Evaluate side-chains 39 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 32 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 0.0370 chunk 43 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 0.0370 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 48 optimal weight: 0.0370 chunk 28 optimal weight: 0.7980 overall best weight: 0.2614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.189945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.180266 restraints weight = 5469.656| |-----------------------------------------------------------------------------| r_work (start): 0.4462 rms_B_bonded: 1.46 r_work: 0.4411 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.4313 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5625 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3946 Z= 0.220 Angle : 0.601 8.229 5414 Z= 0.304 Chirality : 0.044 0.152 644 Planarity : 0.005 0.060 694 Dihedral : 5.623 45.878 583 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.91 % Allowed : 17.15 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.20 % 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: -1.42 (0.37), residues: 520 helix: -0.92 (1.28), residues: 16 sheet: -0.75 (0.35), residues: 228 loop : -1.03 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 106 HIS 0.004 0.001 HIS H 38 PHE 0.009 0.001 PHE H 30 TYR 0.014 0.002 TYR A 272 ARG 0.001 0.000 ARG A 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1552.87 seconds wall clock time: 28 minutes 29.89 seconds (1709.89 seconds total)