Starting phenix.real_space_refine on Wed Mar 5 17:16:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9asd_43813/03_2025/9asd_43813.cif Found real_map, /net/cci-nas-00/data/ceres_data/9asd_43813/03_2025/9asd_43813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9asd_43813/03_2025/9asd_43813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9asd_43813/03_2025/9asd_43813.map" model { file = "/net/cci-nas-00/data/ceres_data/9asd_43813/03_2025/9asd_43813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9asd_43813/03_2025/9asd_43813.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.038 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: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 1964 2.51 5 N 513 2.21 5 O 521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3013 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 837 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 49 Chain: "L" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 738 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "R" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1410 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 13, 'TRANS': 177} Chain breaks: 2 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'HIS:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 55 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.52, per 1000 atoms: 1.83 Number of scatterers: 3013 At special positions: 0 Unit cell: (64, 68, 90, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 521 8.00 N 513 7.00 C 1964 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.09 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.17 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.17 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.04 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.28 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " 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 Links applied NAG-ASN " NAG R1301 " - " ASN R 343 " " NAG R1302 " - " ASN R 354 " Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 368.2 milliseconds 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 10 sheets defined 7.2% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 349 through 353 removed outlier: 3.922A pdb=" N TRP R 353 " --> pdb=" O VAL R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.876A pdb=" N SER R 408 " --> pdb=" O ASN R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.474A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL H 112 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.474A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 10 removed outlier: 6.344A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 10 removed outlier: 6.022A pdb=" N ILE L 98 " --> pdb=" O ALA L 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'R' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'R' and resid 361 through 362 removed outlier: 6.173A pdb=" N CYS R 361 " --> pdb=" O CYS R 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'R' and resid 473 through 474 114 hydrogen bonds defined for protein. 273 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: 0.75 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.26: 476 1.26 - 1.41: 935 1.41 - 1.57: 1670 1.57 - 1.72: 5 1.72 - 1.87: 18 Bond restraints: 3104 Sorted by residual: bond pdb=" C LYS R 403 " pdb=" O LYS R 403 " ideal model delta sigma weight residual 1.234 1.111 0.123 1.25e-02 6.40e+03 9.68e+01 bond pdb=" CA LYS R 403 " pdb=" C LYS R 403 " ideal model delta sigma weight residual 1.524 1.444 0.080 1.31e-02 5.83e+03 3.77e+01 bond pdb=" C LYS R 403 " pdb=" N GLY R 404 " ideal model delta sigma weight residual 1.334 1.262 0.072 1.32e-02 5.74e+03 2.99e+01 bond pdb=" C MET L 49 " pdb=" O MET L 49 " ideal model delta sigma weight residual 1.235 1.187 0.048 1.26e-02 6.30e+03 1.46e+01 bond pdb=" C ILE L 50 " pdb=" O ILE L 50 " ideal model delta sigma weight residual 1.237 1.195 0.042 1.11e-02 8.12e+03 1.42e+01 ... (remaining 3099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 3961 2.53 - 5.06: 209 5.06 - 7.59: 60 7.59 - 10.12: 12 10.12 - 12.65: 4 Bond angle restraints: 4246 Sorted by residual: angle pdb=" N ALA L 82 " pdb=" CA ALA L 82 " pdb=" C ALA L 82 " ideal model delta sigma weight residual 112.38 121.88 -9.50 1.22e+00 6.72e-01 6.06e+01 angle pdb=" N SER R 469 " pdb=" CA SER R 469 " pdb=" C SER R 469 " ideal model delta sigma weight residual 109.40 96.75 12.65 1.63e+00 3.76e-01 6.02e+01 angle pdb=" C GLY R 526 " pdb=" N PRO R 527 " pdb=" CA PRO R 527 " ideal model delta sigma weight residual 119.76 127.64 -7.88 1.03e+00 9.43e-01 5.86e+01 angle pdb=" C TYR H 101 " pdb=" N PRO H 102 " pdb=" CA PRO H 102 " ideal model delta sigma weight residual 120.21 127.29 -7.08 9.60e-01 1.09e+00 5.44e+01 angle pdb=" N ASP L 84 " pdb=" CA ASP L 84 " pdb=" C ASP L 84 " ideal model delta sigma weight residual 113.17 104.03 9.14 1.26e+00 6.30e-01 5.26e+01 ... (remaining 4241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.04: 1666 15.04 - 30.08: 90 30.08 - 45.12: 29 45.12 - 60.15: 5 60.15 - 75.19: 3 Dihedral angle restraints: 1793 sinusoidal: 582 harmonic: 1211 Sorted by residual: dihedral pdb=" C LYS R 403 " pdb=" N LYS R 403 " pdb=" CA LYS R 403 " pdb=" CB LYS R 403 " ideal model delta harmonic sigma weight residual -122.60 -102.68 -19.92 0 2.50e+00 1.60e-01 6.35e+01 dihedral pdb=" N VAL L 53 " pdb=" C VAL L 53 " pdb=" CA VAL L 53 " pdb=" CB VAL L 53 " ideal model delta harmonic sigma weight residual 123.40 140.49 -17.09 0 2.50e+00 1.60e-01 4.67e+01 dihedral pdb=" C ILE R 468 " pdb=" N ILE R 468 " pdb=" CA ILE R 468 " pdb=" CB ILE R 468 " ideal model delta harmonic sigma weight residual -122.00 -106.29 -15.71 0 2.50e+00 1.60e-01 3.95e+01 ... (remaining 1790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 389 0.114 - 0.227: 46 0.227 - 0.340: 8 0.340 - 0.453: 0 0.453 - 0.567: 3 Chirality restraints: 446 Sorted by residual: chirality pdb=" CA VAL L 53 " pdb=" N VAL L 53 " pdb=" C VAL L 53 " pdb=" CB VAL L 53 " both_signs ideal model delta sigma weight residual False 2.44 1.87 0.57 2.00e-01 2.50e+01 8.03e+00 chirality pdb=" CB VAL L 53 " pdb=" CA VAL L 53 " pdb=" CG1 VAL L 53 " pdb=" CG2 VAL L 53 " both_signs ideal model delta sigma weight residual False -2.63 -2.08 -0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" CA ILE R 468 " pdb=" N ILE R 468 " pdb=" C ILE R 468 " pdb=" CB ILE R 468 " both_signs ideal model delta sigma weight residual False 2.43 2.99 -0.55 2.00e-01 2.50e+01 7.61e+00 ... (remaining 443 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 56 " -0.736 9.50e-02 1.11e+02 3.30e-01 6.64e+01 pdb=" NE ARG L 56 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG L 56 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG L 56 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG L 56 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 87 " -0.534 9.50e-02 1.11e+02 2.39e-01 3.52e+01 pdb=" NE ARG H 87 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG H 87 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG H 87 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG H 87 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 402 " 0.021 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C ILE R 402 " -0.070 2.00e-02 2.50e+03 pdb=" O ILE R 402 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS R 403 " 0.024 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1063 2.86 - 3.37: 2296 3.37 - 3.88: 4814 3.88 - 4.39: 5605 4.39 - 4.90: 9585 Nonbonded interactions: 23363 Sorted by model distance: nonbonded pdb=" N LYS R 403 " pdb=" O LYS R 403 " model vdw 2.348 2.496 nonbonded pdb=" O ASN R 417 " pdb=" OD1 ASN R 417 " model vdw 2.382 3.040 nonbonded pdb=" O CYS R 480 " pdb=" C LYS R 481 " model vdw 2.454 3.270 nonbonded pdb=" N GLN R 493 " pdb=" O GLN R 493 " model vdw 2.461 2.496 nonbonded pdb=" OH TYR H 108 " pdb=" O LEU R 455 " model vdw 2.468 3.040 ... (remaining 23358 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: 5.310 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.190 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 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 : 0.011 0.123 3104 Z= 0.688 Angle : 1.506 12.646 4246 Z= 1.022 Chirality : 0.090 0.567 446 Planarity : 0.018 0.330 556 Dihedral : 11.034 75.192 1013 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.35 % Allowed : 4.04 % Favored : 94.62 % Cbeta Deviations : 1.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.39), residues: 409 helix: -4.09 (0.64), residues: 14 sheet: 0.63 (0.39), residues: 143 loop : 0.11 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP H 47 HIS 0.001 0.000 HIS L 41 PHE 0.015 0.003 PHE L 48 TYR 0.038 0.005 TYR L 51 ARG 0.006 0.001 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.333 Fit side-chains REVERT: L 52 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7792 (t70) outliers start: 3 outliers final: 0 residues processed: 56 average time/residue: 0.1946 time to fit residues: 12.8786 Evaluate side-chains 39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.2980 chunk 31 optimal weight: 0.0000 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.0980 chunk 20 optimal weight: 0.0970 chunk 16 optimal weight: 0.0020 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.1980 overall best weight: 0.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 417 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.175455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.161760 restraints weight = 4066.649| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 1.66 r_work: 0.3827 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3104 Z= 0.135 Angle : 0.563 6.039 4246 Z= 0.300 Chirality : 0.047 0.230 446 Planarity : 0.004 0.029 556 Dihedral : 4.749 50.853 508 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.14 % Allowed : 5.38 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.41), residues: 409 helix: -3.56 (1.02), residues: 14 sheet: 0.94 (0.40), residues: 147 loop : 0.30 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.001 0.000 HIS L 41 PHE 0.013 0.002 PHE R 377 TYR 0.020 0.001 TYR H 35 ARG 0.003 0.000 ARG R 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: H 35 TYR cc_start: 0.8788 (m-80) cc_final: 0.8564 (m-80) REVERT: H 110 LEU cc_start: 0.8662 (mt) cc_final: 0.8458 (mt) REVERT: L 52 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7844 (t0) outliers start: 7 outliers final: 1 residues processed: 53 average time/residue: 0.1918 time to fit residues: 11.9733 Evaluate side-chains 44 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain R residue 510 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 0.0030 chunk 38 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 405 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.165120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.150498 restraints weight = 4069.959| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.71 r_work: 0.3706 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3104 Z= 0.299 Angle : 0.615 7.082 4246 Z= 0.322 Chirality : 0.049 0.287 446 Planarity : 0.005 0.042 556 Dihedral : 4.936 52.014 508 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.35 % Allowed : 9.87 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.40), residues: 409 helix: -3.80 (0.82), residues: 14 sheet: 1.07 (0.41), residues: 146 loop : -0.05 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 47 HIS 0.002 0.001 HIS R 339 PHE 0.012 0.002 PHE R 377 TYR 0.021 0.002 TYR H 35 ARG 0.002 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: H 35 TYR cc_start: 0.8993 (m-80) cc_final: 0.8713 (m-80) REVERT: H 110 LEU cc_start: 0.9158 (mt) cc_final: 0.8665 (mt) REVERT: L 52 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7994 (t70) REVERT: L 84 ASP cc_start: 0.8304 (m-30) cc_final: 0.8082 (m-30) REVERT: R 501 TYR cc_start: 0.6978 (m-10) cc_final: 0.6566 (m-10) outliers start: 3 outliers final: 1 residues processed: 47 average time/residue: 0.1789 time to fit residues: 10.2176 Evaluate side-chains 41 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain R residue 510 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 13 optimal weight: 0.0770 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.156019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.139239 restraints weight = 4250.013| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.98 r_work: 0.3548 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3104 Z= 0.325 Angle : 0.626 7.220 4246 Z= 0.326 Chirality : 0.049 0.256 446 Planarity : 0.005 0.048 556 Dihedral : 5.186 54.986 508 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.69 % Allowed : 11.21 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.41), residues: 409 helix: -3.87 (0.76), residues: 14 sheet: 1.25 (0.42), residues: 149 loop : -0.21 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.001 0.001 HIS R 505 PHE 0.012 0.002 PHE L 48 TYR 0.018 0.002 TYR H 35 ARG 0.002 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: H 35 TYR cc_start: 0.9106 (m-80) cc_final: 0.8801 (m-80) REVERT: L 52 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8093 (t70) REVERT: L 84 ASP cc_start: 0.8359 (m-30) cc_final: 0.8141 (m-30) REVERT: R 462 LYS cc_start: 0.8212 (mttt) cc_final: 0.7966 (ttmm) REVERT: R 466 ARG cc_start: 0.8662 (ttp-170) cc_final: 0.8384 (ttp-170) REVERT: R 501 TYR cc_start: 0.7350 (m-10) cc_final: 0.7015 (m-80) outliers start: 6 outliers final: 2 residues processed: 46 average time/residue: 0.1910 time to fit residues: 10.6123 Evaluate side-chains 38 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 510 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 39 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.154228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.137469 restraints weight = 4278.191| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.99 r_work: 0.3525 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 3104 Z= 0.371 Angle : 0.648 7.306 4246 Z= 0.334 Chirality : 0.049 0.244 446 Planarity : 0.005 0.053 556 Dihedral : 5.358 56.554 508 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.69 % Allowed : 11.66 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.40), residues: 409 helix: -3.90 (0.75), residues: 14 sheet: 1.18 (0.41), residues: 149 loop : -0.32 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 47 HIS 0.001 0.001 HIS R 339 PHE 0.013 0.002 PHE L 48 TYR 0.018 0.002 TYR H 35 ARG 0.004 0.001 ARG R 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: L 52 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8038 (t70) REVERT: L 84 ASP cc_start: 0.8388 (m-30) cc_final: 0.8182 (m-30) REVERT: R 462 LYS cc_start: 0.8194 (mttt) cc_final: 0.7936 (ttmm) REVERT: R 466 ARG cc_start: 0.8602 (ttp-170) cc_final: 0.8331 (ttp-170) REVERT: R 501 TYR cc_start: 0.7481 (m-10) cc_final: 0.7126 (m-80) outliers start: 6 outliers final: 3 residues processed: 38 average time/residue: 0.2287 time to fit residues: 10.4426 Evaluate side-chains 36 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 510 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 1 optimal weight: 0.0370 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.153728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.136925 restraints weight = 4313.483| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.00 r_work: 0.3518 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 3104 Z= 0.357 Angle : 0.632 7.421 4246 Z= 0.327 Chirality : 0.048 0.238 446 Planarity : 0.005 0.054 556 Dihedral : 5.386 57.709 508 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.69 % Allowed : 12.11 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.40), residues: 409 helix: -3.93 (0.73), residues: 14 sheet: 1.05 (0.41), residues: 149 loop : -0.34 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 47 HIS 0.001 0.001 HIS R 339 PHE 0.012 0.002 PHE R 400 TYR 0.019 0.002 TYR R 451 ARG 0.004 0.001 ARG R 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.344 Fit side-chains REVERT: L 52 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8065 (t70) REVERT: R 380 TYR cc_start: 0.8437 (m-10) cc_final: 0.8215 (m-10) outliers start: 6 outliers final: 2 residues processed: 38 average time/residue: 0.1903 time to fit residues: 8.7177 Evaluate side-chains 34 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain R residue 510 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 22 optimal weight: 0.0770 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 0.0970 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 16 GLN L 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.156114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.139548 restraints weight = 4212.935| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.97 r_work: 0.3546 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3104 Z= 0.213 Angle : 0.565 6.669 4246 Z= 0.293 Chirality : 0.046 0.228 446 Planarity : 0.004 0.052 556 Dihedral : 5.077 58.274 508 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.91 % Favored : 95.84 % Rotamer: Outliers : 2.24 % Allowed : 12.11 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.41), residues: 409 helix: -3.88 (0.73), residues: 14 sheet: 1.15 (0.41), residues: 148 loop : -0.25 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.001 0.000 HIS R 339 PHE 0.012 0.001 PHE R 400 TYR 0.013 0.001 TYR H 108 ARG 0.004 0.000 ARG R 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: H 110 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8647 (mt) REVERT: L 52 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8006 (t70) REVERT: R 462 LYS cc_start: 0.8230 (mttt) cc_final: 0.7965 (ttmm) outliers start: 5 outliers final: 3 residues processed: 42 average time/residue: 0.2093 time to fit residues: 10.4672 Evaluate side-chains 40 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain R residue 510 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.152682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.135860 restraints weight = 4265.950| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.00 r_work: 0.3500 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 3104 Z= 0.408 Angle : 0.651 7.555 4246 Z= 0.336 Chirality : 0.049 0.242 446 Planarity : 0.005 0.054 556 Dihedral : 5.472 58.066 508 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.89 % Favored : 94.87 % Rotamer: Outliers : 2.24 % Allowed : 13.90 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.41), residues: 409 helix: -3.79 (0.78), residues: 14 sheet: 0.95 (0.41), residues: 149 loop : -0.36 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.001 0.001 HIS R 339 PHE 0.012 0.002 PHE R 400 TYR 0.020 0.002 TYR H 35 ARG 0.004 0.001 ARG R 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.327 Fit side-chains REVERT: H 87 ARG cc_start: 0.4658 (tpt170) cc_final: 0.4139 (tpt170) REVERT: H 110 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8692 (mt) REVERT: L 52 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8034 (t70) REVERT: R 380 TYR cc_start: 0.8291 (m-10) cc_final: 0.7948 (m-10) outliers start: 5 outliers final: 2 residues processed: 35 average time/residue: 0.1959 time to fit residues: 8.2846 Evaluate side-chains 34 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain R residue 510 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 23 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 0.1980 chunk 22 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.153924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.138940 restraints weight = 4184.339| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.78 r_work: 0.3572 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3104 Z= 0.234 Angle : 0.585 6.935 4246 Z= 0.302 Chirality : 0.047 0.227 446 Planarity : 0.004 0.053 556 Dihedral : 5.204 58.438 508 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.67 % Favored : 96.09 % Rotamer: Outliers : 1.79 % Allowed : 14.35 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.41), residues: 409 helix: -3.85 (0.75), residues: 14 sheet: 0.94 (0.41), residues: 148 loop : -0.26 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.000 0.000 HIS R 339 PHE 0.013 0.001 PHE R 400 TYR 0.019 0.001 TYR H 59 ARG 0.004 0.000 ARG R 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.304 Fit side-chains REVERT: H 87 ARG cc_start: 0.4434 (tpt170) cc_final: 0.4048 (tpt170) REVERT: L 52 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7923 (t70) REVERT: R 462 LYS cc_start: 0.8190 (mttt) cc_final: 0.7933 (ttmm) outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 0.2032 time to fit residues: 8.9838 Evaluate side-chains 35 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain R residue 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 39 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 0.1980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 0.1980 chunk 35 optimal weight: 0.9980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.155185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.138682 restraints weight = 4189.540| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.97 r_work: 0.3536 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 3104 Z= 0.287 Angle : 0.612 7.084 4246 Z= 0.317 Chirality : 0.048 0.231 446 Planarity : 0.004 0.053 556 Dihedral : 5.264 57.264 508 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.16 % Favored : 95.60 % Rotamer: Outliers : 1.35 % Allowed : 14.80 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.41), residues: 409 helix: -3.91 (0.70), residues: 14 sheet: 0.80 (0.41), residues: 148 loop : -0.27 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.001 0.000 HIS R 339 PHE 0.013 0.002 PHE R 400 TYR 0.022 0.002 TYR H 35 ARG 0.004 0.000 ARG R 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.299 Fit side-chains REVERT: H 87 ARG cc_start: 0.4634 (tpt170) cc_final: 0.4165 (tpt170) REVERT: L 52 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8098 (t70) REVERT: R 462 LYS cc_start: 0.8229 (mttt) cc_final: 0.7961 (ttmm) outliers start: 3 outliers final: 2 residues processed: 40 average time/residue: 0.2078 time to fit residues: 9.8328 Evaluate side-chains 38 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain R residue 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.153277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.136697 restraints weight = 4257.770| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.97 r_work: 0.3520 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 3104 Z= 0.370 Angle : 0.664 7.826 4246 Z= 0.344 Chirality : 0.049 0.236 446 Planarity : 0.005 0.053 556 Dihedral : 5.521 56.399 508 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.65 % Favored : 95.11 % Rotamer: Outliers : 1.35 % Allowed : 15.25 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.40), residues: 409 helix: -3.91 (0.72), residues: 14 sheet: 0.77 (0.41), residues: 143 loop : -0.44 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.001 0.000 HIS R 339 PHE 0.013 0.002 PHE R 377 TYR 0.023 0.002 TYR H 35 ARG 0.004 0.001 ARG R 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2319.52 seconds wall clock time: 40 minutes 31.91 seconds (2431.91 seconds total)