Starting phenix.real_space_refine on Mon Jan 13 15:29:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9asd_43813/01_2025/9asd_43813.cif Found real_map, /net/cci-nas-00/data/ceres_data/9asd_43813/01_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_43813/01_2025/9asd_43813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9asd_43813/01_2025/9asd_43813.map" model { file = "/net/cci-nas-00/data/ceres_data/9asd_43813/01_2025/9asd_43813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9asd_43813/01_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-5571/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: 5.67, per 1000 atoms: 1.88 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: 0.71 Conformation dependent library (CDL) restraints added in 429.5 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: 0.46 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: 0.92 Time building geometry restraints manager: 0.86 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: 7.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 16.010 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.770 ------------------------------------------------------------------------------- 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 : 0.318 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: 0.1913 time to fit residues: 12.6104 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 : 0.338 ------------------------------------------------------------------------------- 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: 0.0040 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: 0.0794 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.176614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.162535 restraints weight = 4092.547| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 1.70 r_work: 0.3826 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3104 Z= 0.135 Angle : 0.561 5.957 4246 Z= 0.299 Chirality : 0.047 0.221 446 Planarity : 0.004 0.029 556 Dihedral : 4.715 50.691 508 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.69 % Allowed : 5.83 % 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: 0.50 (0.41), residues: 409 helix: -3.53 (1.04), residues: 14 sheet: 0.95 (0.41), residues: 147 loop : 0.28 (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 0.021 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 54 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: H 35 TYR cc_start: 0.8744 (m-80) cc_final: 0.8513 (m-80) REVERT: L 52 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7848 (t0) outliers start: 6 outliers final: 1 residues processed: 52 average time/residue: 0.1964 time to fit residues: 12.0470 Evaluate side-chains 43 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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: 0.0670 chunk 38 optimal weight: 0.0870 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.164846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.150260 restraints weight = 4055.418| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.71 r_work: 0.3705 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3104 Z= 0.286 Angle : 0.613 6.979 4246 Z= 0.321 Chirality : 0.049 0.284 446 Planarity : 0.005 0.039 556 Dihedral : 4.908 51.743 508 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % 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: 0.30 (0.40), residues: 409 helix: -3.71 (0.88), residues: 14 sheet: 1.14 (0.41), residues: 145 loop : -0.10 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 47 HIS 0.002 0.001 HIS R 505 PHE 0.011 0.002 PHE L 48 TYR 0.022 0.002 TYR H 35 ARG 0.002 0.001 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 44 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: L 52 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7988 (t70) REVERT: L 84 ASP cc_start: 0.8303 (m-30) cc_final: 0.8077 (m-30) REVERT: R 501 TYR cc_start: 0.6920 (m-10) cc_final: 0.6575 (m-10) outliers start: 3 outliers final: 1 residues processed: 44 average time/residue: 0.1601 time to fit residues: 8.6080 Evaluate side-chains 39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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: 0.6980 chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 13 optimal weight: 0.0170 chunk 1 optimal weight: 0.0770 chunk 28 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 overall best weight: 0.3976 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.164730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.149791 restraints weight = 4105.078| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.75 r_work: 0.3686 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3104 Z= 0.246 Angle : 0.584 6.911 4246 Z= 0.303 Chirality : 0.048 0.244 446 Planarity : 0.004 0.041 556 Dihedral : 4.886 54.095 508 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.24 % Allowed : 10.76 % Favored : 87.00 % 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: 0.36 (0.41), residues: 409 helix: -3.77 (0.77), residues: 14 sheet: 1.22 (0.41), residues: 151 loop : -0.12 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.001 0.001 HIS R 505 PHE 0.012 0.002 PHE R 400 TYR 0.033 0.002 TYR H 35 ARG 0.001 0.000 ARG R 346 *********************** 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 48 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: L 52 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8024 (t70) REVERT: L 84 ASP cc_start: 0.8327 (m-30) cc_final: 0.8096 (m-30) REVERT: R 462 LYS cc_start: 0.8263 (mttt) cc_final: 0.8018 (ttmm) outliers start: 5 outliers final: 1 residues processed: 48 average time/residue: 0.1899 time to fit residues: 10.9523 Evaluate side-chains 42 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 ASP 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: 0.9980 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.153942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.137300 restraints weight = 4291.437| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.97 r_work: 0.3527 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 3104 Z= 0.448 Angle : 0.697 8.467 4246 Z= 0.355 Chirality : 0.052 0.287 446 Planarity : 0.005 0.055 556 Dihedral : 5.408 54.784 508 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.24 % Allowed : 11.21 % Favored : 86.55 % 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: 0.14 (0.40), residues: 409 helix: -3.82 (0.80), residues: 14 sheet: 1.19 (0.42), residues: 149 loop : -0.34 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.002 0.001 HIS R 339 PHE 0.014 0.002 PHE L 48 TYR 0.036 0.003 TYR H 35 ARG 0.003 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 38 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: L 52 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8013 (t70) REVERT: L 84 ASP cc_start: 0.8448 (m-30) cc_final: 0.8235 (m-30) REVERT: R 462 LYS cc_start: 0.8206 (mttt) cc_final: 0.7950 (ttmm) REVERT: R 466 ARG cc_start: 0.8670 (ttp-170) cc_final: 0.8416 (ttp-170) outliers start: 5 outliers final: 3 residues processed: 37 average time/residue: 0.2078 time to fit residues: 9.1879 Evaluate side-chains 37 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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: 0.9980 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 16 optimal weight: 0.0050 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.154724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.138018 restraints weight = 4298.347| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.99 r_work: 0.3538 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3104 Z= 0.311 Angle : 0.620 7.135 4246 Z= 0.319 Chirality : 0.048 0.237 446 Planarity : 0.005 0.054 556 Dihedral : 5.241 56.310 508 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.69 % Allowed : 12.56 % Favored : 84.75 % 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 (0.41), residues: 409 helix: -3.95 (0.74), residues: 14 sheet: 1.05 (0.42), residues: 149 loop : -0.33 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.001 0.001 HIS R 339 PHE 0.012 0.002 PHE R 400 TYR 0.029 0.002 TYR H 35 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 41 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.353 Fit side-chains REVERT: L 52 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8056 (t70) REVERT: L 84 ASP cc_start: 0.8395 (m-30) cc_final: 0.8191 (m-30) REVERT: R 462 LYS cc_start: 0.8218 (mttt) cc_final: 0.7955 (ttmm) outliers start: 6 outliers final: 3 residues processed: 40 average time/residue: 0.1970 time to fit residues: 9.4151 Evaluate side-chains 37 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 22 optimal weight: 0.0050 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.154192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.137505 restraints weight = 4253.986| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.98 r_work: 0.3523 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3830 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= 0.359 Angle : 0.648 7.501 4246 Z= 0.331 Chirality : 0.049 0.241 446 Planarity : 0.005 0.055 556 Dihedral : 5.377 56.629 508 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.65 % Favored : 95.11 % 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: -0.01 (0.40), residues: 409 helix: -3.96 (0.73), residues: 14 sheet: 0.97 (0.41), residues: 149 loop : -0.37 (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 L 48 TYR 0.028 0.002 TYR H 35 ARG 0.004 0.001 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 39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: L 52 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8037 (t70) REVERT: R 462 LYS cc_start: 0.8223 (mttt) cc_final: 0.7955 (ttmm) outliers start: 5 outliers final: 2 residues processed: 38 average time/residue: 0.1949 time to fit residues: 8.8771 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 : 0.318 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 16 optimal weight: 0.0370 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 39 optimal weight: 0.0980 overall best weight: 0.3858 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.155759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.139133 restraints weight = 4247.268| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.98 r_work: 0.3546 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3104 Z= 0.251 Angle : 0.594 6.883 4246 Z= 0.304 Chirality : 0.047 0.230 446 Planarity : 0.004 0.054 556 Dihedral : 5.135 56.999 508 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.91 % Favored : 95.84 % 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: 0.10 (0.41), residues: 409 helix: -3.95 (0.74), residues: 14 sheet: 1.09 (0.41), residues: 148 loop : -0.31 (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 0.023 0.002 TYR H 35 ARG 0.004 0.000 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 38 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.289 Fit side-chains REVERT: L 52 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8049 (t70) REVERT: R 462 LYS cc_start: 0.8228 (mttt) cc_final: 0.7967 (ttmm) outliers start: 4 outliers final: 3 residues processed: 37 average time/residue: 0.2086 time to fit residues: 9.1344 Evaluate side-chains 37 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 MET 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: 0.5980 chunk 28 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 23 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.155346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.138782 restraints weight = 4270.606| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.98 r_work: 0.3542 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3104 Z= 0.281 Angle : 0.612 6.939 4246 Z= 0.314 Chirality : 0.047 0.232 446 Planarity : 0.005 0.054 556 Dihedral : 5.186 56.712 508 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.65 % Favored : 95.11 % Rotamer: Outliers : 1.79 % Allowed : 14.80 % 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: 0.07 (0.41), residues: 409 helix: -3.93 (0.72), residues: 14 sheet: 1.15 (0.42), residues: 142 loop : -0.35 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.001 0.000 HIS R 339 PHE 0.013 0.001 PHE R 400 TYR 0.024 0.002 TYR H 35 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 : 0.310 Fit side-chains revert: symmetry clash REVERT: H 87 ARG cc_start: 0.4486 (tpt170) cc_final: 0.4168 (tpt170) REVERT: L 52 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.8035 (t70) REVERT: R 462 LYS cc_start: 0.8224 (mttt) cc_final: 0.7959 (ttmm) outliers start: 4 outliers final: 3 residues processed: 37 average time/residue: 0.1989 time to fit residues: 8.8171 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 : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 MET 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: 0.6980 chunk 3 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.154771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.138332 restraints weight = 4196.149| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.96 r_work: 0.3527 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 3104 Z= 0.344 Angle : 0.655 7.446 4246 Z= 0.337 Chirality : 0.049 0.239 446 Planarity : 0.005 0.054 556 Dihedral : 5.367 55.339 508 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.40 % Favored : 95.35 % Rotamer: Outliers : 1.79 % Allowed : 16.14 % Favored : 82.06 % 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: -0.08 (0.40), residues: 409 helix: -3.92 (0.73), residues: 14 sheet: 0.97 (0.42), residues: 142 loop : -0.42 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.001 0.001 HIS R 339 PHE 0.012 0.002 PHE R 400 TYR 0.025 0.002 TYR H 35 ARG 0.004 0.001 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 38 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: H 87 ARG cc_start: 0.4576 (tpt170) cc_final: 0.4266 (tpt170) REVERT: L 52 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8116 (t70) REVERT: R 462 LYS cc_start: 0.8215 (mttt) cc_final: 0.7949 (ttmm) outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 0.2247 time to fit residues: 9.8686 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 : 0.338 ------------------------------------------------------------------------------- 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: 0.0570 chunk 23 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 26 optimal weight: 0.0470 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.2980 overall best weight: 0.2796 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.157551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.141196 restraints weight = 4243.600| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.94 r_work: 0.3579 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 3104 Z= 0.250 Angle : 0.649 14.474 4246 Z= 0.329 Chirality : 0.048 0.225 446 Planarity : 0.004 0.052 556 Dihedral : 5.104 55.230 508 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.67 % Favored : 96.09 % Rotamer: Outliers : 1.79 % Allowed : 15.70 % Favored : 82.51 % 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: -0.00 (0.41), residues: 409 helix: -3.88 (0.76), residues: 14 sheet: 0.84 (0.41), residues: 148 loop : -0.25 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.001 0.000 HIS R 505 PHE 0.013 0.001 PHE R 400 TYR 0.021 0.001 TYR H 35 ARG 0.004 0.000 ARG R 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2315.34 seconds wall clock time: 41 minutes 49.35 seconds (2509.35 seconds total)