Starting phenix.real_space_refine on Mon Sep 23 16:45:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaf_36126/09_2024/8jaf_36126.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaf_36126/09_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_36126/09_2024/8jaf_36126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaf_36126/09_2024/8jaf_36126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaf_36126/09_2024/8jaf_36126.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaf_36126/09_2024/8jaf_36126.cif" } 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. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 3.90, per 1000 atoms: 1.01 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 - 3.00 Amino acid : True - 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: 1.12 Conformation dependent library (CDL) restraints added in 513.0 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... Secondary structure from input PDB file: 6 helices and 13 sheets defined 5.6% alpha, 41.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 98 through 108 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 277 through 282 removed outlier: 4.184A pdb=" N ASN A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 57 through 59 No H-bonds generated for 'chain 'H' and resid 57 through 59' Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 105 through 107 No H-bonds generated for 'chain 'H' and resid 105 through 107' Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 9 Processing sheet with id=AA2, 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=AA3, first strand: chain 'A' and resid 26 through 28 removed outlier: 5.870A pdb=" N PHE A 27 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL A 55 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASN A 83 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 57 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL A 81 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N CYS A 59 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA5, 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=AA6, first strand: chain 'A' and resid 207 through 209 removed outlier: 7.270A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE A 233 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N MET A 255 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL A 235 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Processing sheet with id=AA7, 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=AA8, first strand: chain 'H' and resid 62 through 63 removed outlier: 5.798A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL H 96 " --> pdb=" O GLN H 42 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N CYS H 99 " --> pdb=" O TRP H 113 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TRP H 113 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG H 101 " --> pdb=" O ASP H 111 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 62 through 63 removed outlier: 5.798A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL H 96 " --> pdb=" O GLN H 42 " (cutoff:3.500A) Processing sheet with id=AB1, 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=AB2, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.544A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 63 through 64 Processing sheet with id=AB4, first strand: chain 'L' and resid 67 through 68 153 hydrogen bonds defined for protein. 396 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: 1.15 Time building geometry restraints manager: 1.27 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: 0.00 - 2.40: 5251 2.40 - 4.79: 140 4.79 - 7.19: 17 7.19 - 9.59: 1 9.59 - 11.98: 5 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: 698 2.77 - 3.30: 3763 3.30 - 3.83: 6275 3.83 - 4.37: 7107 4.37 - 4.90: 12697 Nonbonded interactions: 30540 Sorted by model distance: nonbonded pdb=" N ILE A 241 " pdb=" O ALA A 247 " model vdw 2.237 3.120 nonbonded pdb=" N TPO V 307 " pdb=" O1P TPO V 307 " model vdw 2.248 3.120 nonbonded pdb=" O PHE A 277 " pdb=" ND2 ASN A 281 " model vdw 2.277 3.120 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 3.120 ... (remaining 30535 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 3.550 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.960 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.640 ------------------------------------------------------------------------------- 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= 0.507 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 : 0.303 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 0.1379 time to fit residues: 7.0732 Evaluate side-chains 34 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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: 2.9990 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 0.0050 overall best weight: 0.3594 ------------------------------------------------------------------------------- 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: 0.5305 moved from start: 0.1507 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= 0.295 Angle : 0.720 6.470 5414 Z= 0.378 Chirality : 0.048 0.154 644 Planarity : 0.006 0.073 694 Dihedral : 7.367 47.652 590 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.03 % Allowed : 6.98 % Favored : 90.99 % 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: -1.79 (0.37), residues: 520 helix: -1.97 (1.05), residues: 16 sheet: -0.89 (0.34), residues: 228 loop : -1.35 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 113 HIS 0.005 0.001 HIS H 38 PHE 0.014 0.002 PHE A 27 TYR 0.016 0.002 TYR H 63 ARG 0.002 0.000 ARG A 52 *********************** 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 40 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.337 Fit side-chains REVERT: A 127 VAL cc_start: 0.7775 (t) cc_final: 0.7453 (p) outliers start: 7 outliers final: 3 residues processed: 38 average time/residue: 0.1288 time to fit residues: 6.7138 Evaluate side-chains 35 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 48 optimal weight: 0.4980 chunk 52 optimal weight: 0.5980 chunk 42 optimal weight: 0.0970 chunk 47 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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: 0.5347 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3946 Z= 0.311 Angle : 0.690 6.817 5414 Z= 0.359 Chirality : 0.047 0.149 644 Planarity : 0.006 0.054 694 Dihedral : 6.380 47.372 583 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.45 % Allowed : 11.05 % Favored : 87.50 % 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: -1.45 (0.38), residues: 520 helix: 0.82 (1.40), residues: 10 sheet: -0.79 (0.35), residues: 235 loop : -1.11 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP H 113 HIS 0.006 0.002 HIS H 38 PHE 0.011 0.002 PHE A 27 TYR 0.025 0.002 TYR H 57 ARG 0.003 0.000 ARG A 76 *********************** 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 37 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 0.396 Fit side-chains REVERT: A 127 VAL cc_start: 0.7810 (t) cc_final: 0.7524 (p) outliers start: 5 outliers final: 4 residues processed: 35 average time/residue: 0.1210 time to fit residues: 6.0528 Evaluate side-chains 37 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 0.0770 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 0.2980 chunk 42 optimal weight: 0.0770 overall best weight: 0.3496 ------------------------------------------------------------------------------- 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: 0.5326 moved from start: 0.2403 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= 0.268 Angle : 0.657 6.757 5414 Z= 0.337 Chirality : 0.046 0.179 644 Planarity : 0.006 0.045 694 Dihedral : 6.079 44.973 583 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.78 % Allowed : 12.50 % Favored : 83.72 % 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: -1.38 (0.38), residues: 520 helix: 1.19 (1.53), residues: 10 sheet: -0.68 (0.35), residues: 224 loop : -1.15 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 113 HIS 0.006 0.002 HIS A 219 PHE 0.009 0.002 PHE A 27 TYR 0.021 0.002 TYR H 57 ARG 0.002 0.000 ARG A 76 *********************** 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 45 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 32 time to evaluate : 0.397 Fit side-chains REVERT: A 127 VAL cc_start: 0.7823 (t) cc_final: 0.7553 (p) outliers start: 13 outliers final: 7 residues processed: 40 average time/residue: 0.1005 time to fit residues: 6.0010 Evaluate side-chains 38 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 92 GLU Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 34 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 45 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.5479 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 3946 Z= 0.520 Angle : 0.835 8.314 5414 Z= 0.431 Chirality : 0.052 0.159 644 Planarity : 0.007 0.055 694 Dihedral : 6.972 40.865 583 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 2.91 % Allowed : 16.57 % Favored : 80.52 % 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: -1.96 (0.37), residues: 520 helix: -1.89 (1.08), residues: 16 sheet: -0.90 (0.36), residues: 214 loop : -1.57 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP H 106 HIS 0.012 0.002 HIS A 219 PHE 0.013 0.003 PHE H 30 TYR 0.020 0.003 TYR H 63 ARG 0.005 0.001 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 45 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 35 time to evaluate : 0.359 Fit side-chains REVERT: A 219 HIS cc_start: 0.3045 (OUTLIER) cc_final: 0.2805 (t70) REVERT: L 71 ASP cc_start: 0.5177 (OUTLIER) cc_final: 0.4188 (t70) outliers start: 10 outliers final: 8 residues processed: 43 average time/residue: 0.1453 time to fit residues: 8.2745 Evaluate side-chains 42 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 32 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 219 HIS 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 92 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 42 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 overall best weight: 0.3938 ------------------------------------------------------------------------------- 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: 0.5392 moved from start: 0.2841 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= 0.297 Angle : 0.690 7.260 5414 Z= 0.357 Chirality : 0.046 0.152 644 Planarity : 0.006 0.059 694 Dihedral : 6.329 41.130 583 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.36 % Allowed : 16.28 % Favored : 79.36 % 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: -1.88 (0.37), residues: 520 helix: -1.76 (1.14), residues: 16 sheet: -0.92 (0.35), residues: 223 loop : -1.45 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 113 HIS 0.006 0.002 HIS A 219 PHE 0.010 0.002 PHE H 30 TYR 0.023 0.002 TYR H 57 ARG 0.003 0.001 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 48 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 33 time to evaluate : 0.372 Fit side-chains REVERT: A 352 MET cc_start: 0.7340 (ttm) cc_final: 0.7133 (ttm) REVERT: L 71 ASP cc_start: 0.4903 (OUTLIER) cc_final: 0.4062 (t70) outliers start: 15 outliers final: 11 residues processed: 44 average time/residue: 0.1064 time to fit residues: 6.7558 Evaluate side-chains 44 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 32 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 214 ILE 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 92 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 0.0050 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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: 0.5465 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 3946 Z= 0.442 Angle : 0.766 7.745 5414 Z= 0.395 Chirality : 0.049 0.153 644 Planarity : 0.007 0.059 694 Dihedral : 6.735 40.930 583 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 4.65 % Allowed : 17.15 % Favored : 78.20 % 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: -2.11 (0.36), residues: 520 helix: -2.07 (1.09), residues: 16 sheet: -1.01 (0.35), residues: 221 loop : -1.67 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP H 106 HIS 0.010 0.002 HIS A 219 PHE 0.013 0.002 PHE H 30 TYR 0.018 0.003 TYR H 57 ARG 0.004 0.001 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 49 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 33 time to evaluate : 0.300 Fit side-chains REVERT: A 219 HIS cc_start: 0.2887 (OUTLIER) cc_final: 0.2546 (t70) REVERT: L 71 ASP cc_start: 0.5021 (OUTLIER) cc_final: 0.4083 (t70) outliers start: 16 outliers final: 13 residues processed: 45 average time/residue: 0.1121 time to fit residues: 6.9624 Evaluate side-chains 46 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 31 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 219 HIS 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 92 GLU 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 Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 25 optimal weight: 0.0870 chunk 4 optimal weight: 0.2980 chunk 40 optimal weight: 0.7980 chunk 46 optimal weight: 0.0770 chunk 48 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 28 optimal weight: 0.3980 overall best weight: 0.2316 ------------------------------------------------------------------------------- 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: 0.5349 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3946 Z= 0.226 Angle : 0.651 8.212 5414 Z= 0.334 Chirality : 0.045 0.163 644 Planarity : 0.006 0.057 694 Dihedral : 6.047 44.630 583 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.91 % Allowed : 19.19 % Favored : 77.91 % 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: 0.12 (1.60), residues: 10 sheet: -0.94 (0.35), residues: 222 loop : -1.31 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 113 HIS 0.004 0.001 HIS H 38 PHE 0.010 0.001 PHE L 99 TYR 0.010 0.002 TYR H 57 ARG 0.003 0.000 ARG H 70 *********************** 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 42 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 32 time to evaluate : 0.437 Fit side-chains REVERT: A 127 VAL cc_start: 0.7777 (t) cc_final: 0.7547 (p) REVERT: L 71 ASP cc_start: 0.4720 (OUTLIER) cc_final: 0.3968 (t70) outliers start: 10 outliers final: 8 residues processed: 40 average time/residue: 0.1236 time to fit residues: 6.9370 Evaluate side-chains 40 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 31 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 92 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 47 optimal weight: 0.0060 chunk 31 optimal weight: 0.1980 chunk 50 optimal weight: 0.4980 chunk 30 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- 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: 0.5368 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3946 Z= 0.259 Angle : 0.665 8.488 5414 Z= 0.338 Chirality : 0.046 0.149 644 Planarity : 0.006 0.055 694 Dihedral : 6.042 44.012 583 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.20 % Allowed : 18.90 % Favored : 77.91 % 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: -1.70 (0.37), residues: 520 helix: 0.16 (1.63), residues: 10 sheet: -0.96 (0.34), residues: 227 loop : -1.27 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 106 HIS 0.005 0.001 HIS A 219 PHE 0.009 0.001 PHE H 30 TYR 0.010 0.002 TYR H 63 ARG 0.002 0.000 ARG A 52 *********************** 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 40 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 29 time to evaluate : 0.397 Fit side-chains REVERT: L 71 ASP cc_start: 0.4814 (OUTLIER) cc_final: 0.3994 (t70) outliers start: 11 outliers final: 8 residues processed: 38 average time/residue: 0.1113 time to fit residues: 6.1997 Evaluate side-chains 38 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 29 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 92 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 0.0570 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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: 0.5416 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3946 Z= 0.341 Angle : 0.711 7.672 5414 Z= 0.363 Chirality : 0.048 0.172 644 Planarity : 0.006 0.056 694 Dihedral : 6.336 42.809 583 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.91 % Allowed : 18.31 % Favored : 78.78 % 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: -1.82 (0.37), residues: 520 helix: -0.08 (1.61), residues: 10 sheet: -1.03 (0.34), residues: 228 loop : -1.36 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP H 106 HIS 0.007 0.002 HIS A 219 PHE 0.012 0.002 PHE H 30 TYR 0.015 0.002 TYR H 57 ARG 0.003 0.001 ARG A 52 ********************** 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 40 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 30 time to evaluate : 0.395 Fit side-chains REVERT: L 71 ASP cc_start: 0.4793 (OUTLIER) cc_final: 0.3905 (t70) outliers start: 10 outliers final: 9 residues processed: 39 average time/residue: 0.1089 time to fit residues: 6.1362 Evaluate side-chains 40 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 30 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 92 GLU 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 11 optimal weight: 0.0980 chunk 42 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 0.0170 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 36 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 0.0870 chunk 28 optimal weight: 0.3980 overall best weight: 0.1196 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.192558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.182576 restraints weight = 5376.946| |-----------------------------------------------------------------------------| r_work (start): 0.4492 rms_B_bonded: 1.54 r_work: 0.4441 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.4343 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.4343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5587 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3946 Z= 0.180 Angle : 0.603 8.815 5414 Z= 0.306 Chirality : 0.044 0.146 644 Planarity : 0.005 0.055 694 Dihedral : 5.700 49.255 583 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.33 % Allowed : 19.19 % Favored : 78.49 % 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 (0.37), residues: 520 helix: 0.22 (1.65), residues: 10 sheet: -0.78 (0.35), residues: 224 loop : -1.18 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 106 HIS 0.003 0.001 HIS A 198 PHE 0.011 0.001 PHE A 115 TYR 0.014 0.001 TYR H 57 ARG 0.002 0.000 ARG H 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1516.73 seconds wall clock time: 31 minutes 0.92 seconds (1860.92 seconds total)