Starting phenix.real_space_refine on Wed Jul 1 23:21:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9obt_70298/07_2026/9obt_70298.cif Found real_map, /net/cci-nas-00/data/ceres_data/9obt_70298/07_2026/9obt_70298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9obt_70298/07_2026/9obt_70298.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9obt_70298/07_2026/9obt_70298.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9obt_70298/07_2026/9obt_70298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9obt_70298/07_2026/9obt_70298.map" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 28 5.16 5 C 2668 2.51 5 N 574 2.21 5 O 680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3954 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 905 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2, 'GLU:plan': 3, 'PHE:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 926 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain breaks: 2 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 905 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2, 'GLU:plan': 3, 'PHE:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 926 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain breaks: 2 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 1.12, per 1000 atoms: 0.28 Number of scatterers: 3954 At special positions: 0 Unit cell: (70.295, 73.603, 66.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 4 15.00 O 680 8.00 N 574 7.00 C 2668 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 161.0 milliseconds 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 956 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 79.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 559 through 583 removed outlier: 3.920A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 615 Processing helix chain 'A' and resid 626 through 657 Processing helix chain 'A' and resid 809 through 840 removed outlier: 5.200A pdb=" N GLY A 815 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A 832 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE A 833 " --> pdb=" O PHE A 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 552 removed outlier: 3.519A pdb=" N LEU B 551 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU B 552 " --> pdb=" O ALA B 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 548 through 552' Processing helix chain 'B' and resid 555 through 579 removed outlier: 3.517A pdb=" N TYR B 579 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 removed outlier: 3.509A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 656 Processing helix chain 'B' and resid 816 through 818 No H-bonds generated for 'chain 'B' and resid 816 through 818' Processing helix chain 'B' and resid 819 through 841 removed outlier: 3.670A pdb=" N LEU B 841 " --> pdb=" O ILE B 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 583 removed outlier: 3.886A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 615 Processing helix chain 'C' and resid 626 through 657 Processing helix chain 'C' and resid 809 through 840 removed outlier: 5.182A pdb=" N GLY C 815 " --> pdb=" O GLU C 811 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL C 816 " --> pdb=" O ASN C 812 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU C 819 " --> pdb=" O GLY C 815 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE C 832 " --> pdb=" O ILE C 828 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE C 833 " --> pdb=" O PHE C 829 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 552 removed outlier: 3.518A pdb=" N LEU D 551 " --> pdb=" O SER D 548 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D 552 " --> pdb=" O ALA D 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 548 through 552' Processing helix chain 'D' and resid 555 through 579 removed outlier: 3.514A pdb=" N TYR D 579 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 614 removed outlier: 3.509A pdb=" N PHE D 614 " --> pdb=" O TRP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 656 Processing helix chain 'D' and resid 816 through 818 No H-bonds generated for 'chain 'D' and resid 816 through 818' Processing helix chain 'D' and resid 819 through 841 removed outlier: 3.663A pdb=" N LEU D 841 " --> pdb=" O ILE D 837 " (cutoff:3.500A) 308 hydrogen bonds defined for protein. 924 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: 0.44 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 569 1.32 - 1.44: 1093 1.44 - 1.56: 2288 1.56 - 1.68: 8 1.68 - 1.80: 56 Bond restraints: 4014 Sorted by residual: bond pdb=" C GLU B 552 " pdb=" N PRO B 553 " ideal model delta sigma weight residual 1.334 1.345 -0.011 1.51e-02 4.39e+03 5.02e-01 bond pdb=" CB PRO B 553 " pdb=" CG PRO B 553 " ideal model delta sigma weight residual 1.492 1.459 0.033 5.00e-02 4.00e+02 4.34e-01 bond pdb=" CB PRO D 553 " pdb=" CG PRO D 553 " ideal model delta sigma weight residual 1.492 1.459 0.033 5.00e-02 4.00e+02 4.34e-01 bond pdb=" C GLU D 552 " pdb=" N PRO D 553 " ideal model delta sigma weight residual 1.334 1.344 -0.009 1.51e-02 4.39e+03 3.80e-01 bond pdb=" CA GLU D 552 " pdb=" C GLU D 552 " ideal model delta sigma weight residual 1.524 1.531 -0.007 1.26e-02 6.30e+03 2.84e-01 ... (remaining 4009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 5338 1.05 - 2.09: 83 2.09 - 3.14: 16 3.14 - 4.18: 7 4.18 - 5.23: 6 Bond angle restraints: 5450 Sorted by residual: angle pdb=" N GLU D 552 " pdb=" CA GLU D 552 " pdb=" C GLU D 552 " ideal model delta sigma weight residual 109.81 115.04 -5.23 2.21e+00 2.05e-01 5.59e+00 angle pdb=" N GLU B 552 " pdb=" CA GLU B 552 " pdb=" C GLU B 552 " ideal model delta sigma weight residual 109.81 115.01 -5.20 2.21e+00 2.05e-01 5.54e+00 angle pdb=" C PHE D 614 " pdb=" N ASN D 615 " pdb=" CA ASN D 615 " ideal model delta sigma weight residual 121.54 125.72 -4.18 1.91e+00 2.74e-01 4.78e+00 angle pdb=" C PHE B 614 " pdb=" N ASN B 615 " pdb=" CA ASN B 615 " ideal model delta sigma weight residual 121.54 125.71 -4.17 1.91e+00 2.74e-01 4.76e+00 angle pdb=" C PHE D 842 " pdb=" CA PHE D 842 " pdb=" CB PHE D 842 " ideal model delta sigma weight residual 110.10 112.95 -2.85 1.90e+00 2.77e-01 2.24e+00 ... (remaining 5445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 2234 15.89 - 31.78: 112 31.78 - 47.68: 31 47.68 - 63.57: 21 63.57 - 79.46: 10 Dihedral angle restraints: 2408 sinusoidal: 946 harmonic: 1462 Sorted by residual: dihedral pdb=" CB MET D 631 " pdb=" CG MET D 631 " pdb=" SD MET D 631 " pdb=" CE MET D 631 " ideal model delta sinusoidal sigma weight residual -180.00 -130.54 -49.46 3 1.50e+01 4.44e-03 8.78e+00 dihedral pdb=" CB MET B 631 " pdb=" CG MET B 631 " pdb=" SD MET B 631 " pdb=" CE MET B 631 " ideal model delta sinusoidal sigma weight residual -180.00 -131.14 -48.86 3 1.50e+01 4.44e-03 8.70e+00 dihedral pdb=" N MET D 818 " pdb=" CA MET D 818 " pdb=" CB MET D 818 " pdb=" CG MET D 818 " ideal model delta sinusoidal sigma weight residual -180.00 -141.66 -38.34 3 1.50e+01 4.44e-03 6.75e+00 ... (remaining 2405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 362 0.024 - 0.047: 181 0.047 - 0.071: 93 0.071 - 0.094: 3 0.094 - 0.118: 11 Chirality restraints: 650 Sorted by residual: chirality pdb=" CA PRO D 553 " pdb=" N PRO D 553 " pdb=" C PRO D 553 " pdb=" CB PRO D 553 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.47e-01 chirality pdb=" CA PRO B 553 " pdb=" N PRO B 553 " pdb=" C PRO B 553 " pdb=" CB PRO B 553 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.38e-01 chirality pdb=" CA PRO C 557 " pdb=" N PRO C 557 " pdb=" C PRO C 557 " pdb=" CB PRO C 557 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.12e-01 ... (remaining 647 not shown) Planarity restraints: 626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 552 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO B 553 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 553 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 553 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 552 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.72e+00 pdb=" N PRO D 553 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 553 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 553 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 618 " 0.017 5.00e-02 4.00e+02 2.54e-02 1.03e+00 pdb=" N PRO B 619 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 619 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 619 " 0.014 5.00e-02 4.00e+02 ... (remaining 623 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 928 2.78 - 3.31: 3790 3.31 - 3.84: 6319 3.84 - 4.37: 7812 4.37 - 4.90: 13380 Nonbonded interactions: 32229 Sorted by model distance: nonbonded pdb=" O SER D 617 " pdb=" O HOH D1001 " model vdw 2.253 3.040 nonbonded pdb=" O SER B 617 " pdb=" O HOH B1001 " model vdw 2.254 3.040 nonbonded pdb=" O SER D 599 " pdb=" NZ LYS D 604 " model vdw 2.335 3.120 nonbonded pdb=" O SER B 599 " pdb=" NZ LYS B 604 " model vdw 2.335 3.120 nonbonded pdb=" ND2 ASN D 615 " pdb=" O HOH D1002 " model vdw 2.384 3.120 ... (remaining 32224 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 7.510 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.360 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4014 Z= 0.111 Angle : 0.417 5.227 5450 Z= 0.222 Chirality : 0.033 0.118 650 Planarity : 0.003 0.033 626 Dihedral : 13.109 79.461 1452 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.47 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.34), residues: 486 helix: 0.59 (0.23), residues: 366 sheet: None (None), residues: 0 loop : -0.84 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 625 TYR 0.002 0.001 TYR C 647 PHE 0.007 0.001 PHE D 614 TRP 0.006 0.001 TRP B 607 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 4014) covalent geometry : angle 0.41711 / 0.22 ( 5450) hydrogen bonds : bond 0.23232 / 15.31 ( 308) hydrogen bonds : angle 5.97314 / 4.22 ( 924) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.131 Fit side-chains REVERT: B 829 MET cc_start: 0.8634 (mtt) cc_final: 0.8390 (mtt) REVERT: D 829 MET cc_start: 0.8619 (mtt) cc_final: 0.8376 (mtt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0391 time to fit residues: 4.3818 Evaluate side-chains 59 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 812 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.136126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.109110 restraints weight = 4397.033| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.51 r_work: 0.2932 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4014 Z= 0.168 Angle : 0.485 5.384 5450 Z= 0.259 Chirality : 0.037 0.122 650 Planarity : 0.004 0.035 626 Dihedral : 13.929 83.739 812 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.88 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.36), residues: 486 helix: 1.98 (0.24), residues: 384 sheet: None (None), residues: 0 loop : -0.23 (0.66), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 625 TYR 0.003 0.001 TYR C 647 PHE 0.010 0.001 PHE D 642 TRP 0.009 0.001 TRP C 563 HIS 0.001 0.000 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 4014) covalent geometry : angle 0.48473 / 0.26 ( 5450) hydrogen bonds : bond 0.05356 / 3.45 ( 308) hydrogen bonds : angle 3.56020 / 2.58 ( 924) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.135 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0429 time to fit residues: 3.2333 Evaluate side-chains 52 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 19 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.135915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.109075 restraints weight = 4298.515| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.48 r_work: 0.2925 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4014 Z= 0.172 Angle : 0.474 5.376 5450 Z= 0.249 Chirality : 0.036 0.123 650 Planarity : 0.004 0.035 626 Dihedral : 13.825 86.640 812 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.47 % Favored : 97.12 % Rotamer: Outliers : 0.58 % Allowed : 5.26 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.36), residues: 486 helix: 2.37 (0.24), residues: 386 sheet: None (None), residues: 0 loop : -0.13 (0.68), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 625 TYR 0.004 0.001 TYR C 647 PHE 0.010 0.001 PHE D 642 TRP 0.009 0.001 TRP C 563 HIS 0.001 0.000 HIS C 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 ( 4014) covalent geometry : angle 0.47359 / 0.25 ( 5450) hydrogen bonds : bond 0.04936 / 3.18 ( 308) hydrogen bonds : angle 3.40548 / 2.47 ( 924) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.139 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 51 average time/residue: 0.0437 time to fit residues: 3.2250 Evaluate side-chains 51 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain C residue 626 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 35 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 0.1980 chunk 34 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.134307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.106274 restraints weight = 4308.825| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.58 r_work: 0.2920 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4014 Z= 0.146 Angle : 0.441 5.298 5450 Z= 0.232 Chirality : 0.035 0.120 650 Planarity : 0.004 0.035 626 Dihedral : 13.473 88.572 812 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.88 % Favored : 96.71 % Rotamer: Outliers : 0.88 % Allowed : 4.39 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.21 (0.36), residues: 486 helix: 2.67 (0.24), residues: 386 sheet: None (None), residues: 0 loop : -0.10 (0.67), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 625 TYR 0.003 0.001 TYR C 647 PHE 0.010 0.001 PHE B 642 TRP 0.009 0.001 TRP C 563 HIS 0.000 0.000 HIS C 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 4014) covalent geometry : angle 0.44120 / 0.23 ( 5450) hydrogen bonds : bond 0.04431 / 2.84 ( 308) hydrogen bonds : angle 3.23235 / 2.35 ( 924) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.153 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 53 average time/residue: 0.0449 time to fit residues: 3.4618 Evaluate side-chains 53 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain C residue 626 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 23 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.0970 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 chunk 19 optimal weight: 0.5980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.136099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.108061 restraints weight = 4273.179| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.57 r_work: 0.2953 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4014 Z= 0.119 Angle : 0.409 5.242 5450 Z= 0.215 Chirality : 0.034 0.116 650 Planarity : 0.003 0.034 626 Dihedral : 12.999 88.604 812 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.17 % Allowed : 4.39 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.58 (0.37), residues: 486 helix: 2.94 (0.24), residues: 386 sheet: None (None), residues: 0 loop : -0.03 (0.67), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 625 TYR 0.003 0.001 TYR A 647 PHE 0.009 0.001 PHE B 642 TRP 0.008 0.001 TRP C 563 HIS 0.001 0.001 HIS C 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 4014) covalent geometry : angle 0.40920 / 0.21 ( 5450) hydrogen bonds : bond 0.04041 / 2.59 ( 308) hydrogen bonds : angle 3.08038 / 2.24 ( 924) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.134 Fit side-chains REVERT: A 556 GLN cc_start: 0.9023 (tp40) cc_final: 0.8733 (tp40) outliers start: 4 outliers final: 4 residues processed: 57 average time/residue: 0.0418 time to fit residues: 3.4653 Evaluate side-chains 57 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 628 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.1980 chunk 44 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.135659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.108313 restraints weight = 4334.110| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.52 r_work: 0.2936 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4014 Z= 0.136 Angle : 0.428 5.271 5450 Z= 0.224 Chirality : 0.035 0.119 650 Planarity : 0.004 0.035 626 Dihedral : 13.147 89.297 812 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.88 % Allowed : 5.56 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.54 (0.37), residues: 486 helix: 2.91 (0.24), residues: 386 sheet: None (None), residues: 0 loop : -0.07 (0.68), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 630 TYR 0.003 0.001 TYR A 647 PHE 0.010 0.001 PHE B 642 TRP 0.009 0.001 TRP C 563 HIS 0.000 0.000 HIS C 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 4014) covalent geometry : angle 0.42801 / 0.22 ( 5450) hydrogen bonds : bond 0.04268 / 2.74 ( 308) hydrogen bonds : angle 3.13031 / 2.27 ( 924) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.128 Fit side-chains REVERT: A 556 GLN cc_start: 0.9011 (tp40) cc_final: 0.8717 (tp40) outliers start: 3 outliers final: 1 residues processed: 54 average time/residue: 0.0428 time to fit residues: 3.3494 Evaluate side-chains 52 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.134776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.107502 restraints weight = 4318.460| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.51 r_work: 0.2931 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4014 Z= 0.159 Angle : 0.448 5.367 5450 Z= 0.236 Chirality : 0.036 0.122 650 Planarity : 0.004 0.035 626 Dihedral : 13.275 89.468 812 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.47 % Favored : 97.12 % Rotamer: Outliers : 1.17 % Allowed : 4.68 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.35 (0.37), residues: 486 helix: 2.79 (0.24), residues: 386 sheet: None (None), residues: 0 loop : -0.16 (0.68), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 625 TYR 0.004 0.001 TYR C 647 PHE 0.010 0.001 PHE B 642 TRP 0.009 0.001 TRP C 563 HIS 0.001 0.000 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 4014) covalent geometry : angle 0.44796 / 0.24 ( 5450) hydrogen bonds : bond 0.04539 / 2.92 ( 308) hydrogen bonds : angle 3.22117 / 2.34 ( 924) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.136 Fit side-chains REVERT: A 556 GLN cc_start: 0.9020 (tp40) cc_final: 0.8725 (tp40) REVERT: C 556 GLN cc_start: 0.9020 (tp40) cc_final: 0.8721 (tp40) outliers start: 4 outliers final: 4 residues processed: 55 average time/residue: 0.0418 time to fit residues: 3.3395 Evaluate side-chains 55 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 628 SER Chi-restraints excluded: chain D residue 576 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.136498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.109756 restraints weight = 4266.161| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.48 r_work: 0.2947 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4014 Z= 0.147 Angle : 0.434 5.326 5450 Z= 0.229 Chirality : 0.036 0.121 650 Planarity : 0.004 0.035 626 Dihedral : 13.127 88.108 812 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.47 % Favored : 97.12 % Rotamer: Outliers : 1.17 % Allowed : 4.39 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.40 (0.37), residues: 486 helix: 2.79 (0.24), residues: 388 sheet: None (None), residues: 0 loop : -0.05 (0.69), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 625 TYR 0.003 0.001 TYR A 647 PHE 0.009 0.001 PHE B 642 TRP 0.009 0.001 TRP C 563 HIS 0.000 0.000 HIS C 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 4014) covalent geometry : angle 0.43444 / 0.23 ( 5450) hydrogen bonds : bond 0.04336 / 2.79 ( 308) hydrogen bonds : angle 3.15936 / 2.30 ( 924) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.130 Fit side-chains REVERT: A 556 GLN cc_start: 0.9008 (tp40) cc_final: 0.8711 (tp40) REVERT: C 556 GLN cc_start: 0.9027 (tp40) cc_final: 0.8742 (tp40) outliers start: 4 outliers final: 4 residues processed: 55 average time/residue: 0.0462 time to fit residues: 3.6534 Evaluate side-chains 55 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 628 SER Chi-restraints excluded: chain D residue 576 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 4 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 0.0060 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.138784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.111781 restraints weight = 4308.701| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.52 r_work: 0.2952 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4014 Z= 0.130 Angle : 0.419 5.258 5450 Z= 0.221 Chirality : 0.035 0.118 650 Planarity : 0.004 0.035 626 Dihedral : 12.884 87.933 812 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.58 % Allowed : 4.97 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.55 (0.37), residues: 486 helix: 2.90 (0.24), residues: 388 sheet: None (None), residues: 0 loop : -0.02 (0.69), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 625 TYR 0.003 0.001 TYR A 647 PHE 0.009 0.001 PHE D 642 TRP 0.008 0.001 TRP C 563 HIS 0.001 0.000 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 4014) covalent geometry : angle 0.41943 / 0.22 ( 5450) hydrogen bonds : bond 0.04106 / 2.64 ( 308) hydrogen bonds : angle 3.08181 / 2.24 ( 924) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.140 Fit side-chains REVERT: A 556 GLN cc_start: 0.9029 (tp40) cc_final: 0.8741 (tp40) outliers start: 2 outliers final: 2 residues processed: 55 average time/residue: 0.0343 time to fit residues: 2.7682 Evaluate side-chains 55 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain B residue 576 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.139561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.112453 restraints weight = 4259.528| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.52 r_work: 0.2975 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4014 Z= 0.122 Angle : 0.410 5.254 5450 Z= 0.216 Chirality : 0.035 0.117 650 Planarity : 0.004 0.035 626 Dihedral : 12.663 87.984 812 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.88 % Allowed : 4.68 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.70 (0.37), residues: 486 helix: 3.01 (0.24), residues: 388 sheet: None (None), residues: 0 loop : -0.00 (0.69), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 625 TYR 0.003 0.001 TYR A 647 PHE 0.010 0.001 PHE B 642 TRP 0.008 0.001 TRP C 563 HIS 0.001 0.000 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 4014) covalent geometry : angle 0.40993 / 0.22 ( 5450) hydrogen bonds : bond 0.03951 / 2.53 ( 308) hydrogen bonds : angle 3.01932 / 2.19 ( 924) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.138 Fit side-chains REVERT: A 556 GLN cc_start: 0.9023 (tp40) cc_final: 0.8740 (tp40) REVERT: C 556 GLN cc_start: 0.9052 (tp40) cc_final: 0.8772 (mm-40) outliers start: 3 outliers final: 3 residues processed: 56 average time/residue: 0.0385 time to fit residues: 3.1662 Evaluate side-chains 56 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 628 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 47 optimal weight: 0.5980 chunk 31 optimal weight: 0.0670 chunk 24 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 0.0770 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 0.1980 chunk 22 optimal weight: 0.0870 overall best weight: 0.1054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.147745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.120743 restraints weight = 4309.799| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.57 r_work: 0.3042 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4014 Z= 0.085 Angle : 0.367 5.207 5450 Z= 0.194 Chirality : 0.033 0.105 650 Planarity : 0.003 0.035 626 Dihedral : 11.938 89.689 812 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.50 (0.37), residues: 486 helix: 3.75 (0.23), residues: 374 sheet: None (None), residues: 0 loop : 0.06 (0.66), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 625 TYR 0.002 0.000 TYR C 647 PHE 0.010 0.001 PHE B 642 TRP 0.006 0.001 TRP D 635 HIS 0.003 0.002 HIS C 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00167 / 0.09 ( 4014) covalent geometry : angle 0.36749 / 0.19 ( 5450) hydrogen bonds : bond 0.03090 / 1.97 ( 308) hydrogen bonds : angle 2.70625 / 1.96 ( 924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1259.29 seconds wall clock time: 22 minutes 18.48 seconds (1338.48 seconds total)