Starting phenix.real_space_refine on Wed Jul 1 22:42:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oby_70303/07_2026/9oby_70303.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oby_70303/07_2026/9oby_70303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oby_70303/07_2026/9oby_70303.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oby_70303/07_2026/9oby_70303.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oby_70303/07_2026/9oby_70303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oby_70303/07_2026/9oby_70303.map" } resolution = 3.6 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= 0.007 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 Ca 1 9.91 5 S 23 5.16 5 C 2338 2.51 5 N 562 2.21 5 O 617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 3541 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 841 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 2 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 2, 'TYR:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'PHE:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 906 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain breaks: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 3, 'TYR:plan': 2, 'GLN:plan1': 2, 'ASP:plan': 1, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 871 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2, 'GLU:plan': 3, 'PHE:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 913 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain breaks: 2 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 4, 'TYR:plan': 2, 'GLN:plan1': 3, 'ASP:plan': 1, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 83 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 1.08, per 1000 atoms: 0.30 Number of scatterers: 3541 At special positions: 0 Unit cell: (71.949, 85.181, 64.506, 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) Ca 1 19.99 S 23 16.00 O 617 8.00 N 562 7.00 C 2338 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: 0.20 Conformation dependent library (CDL) restraints added in 131.2 milliseconds 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 73.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 559 through 583 removed outlier: 3.669A pdb=" N ARG A 582 " --> pdb=" O TYR A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 615 removed outlier: 3.687A pdb=" N MET A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 657 Processing helix chain 'A' and resid 814 through 838 removed outlier: 4.276A pdb=" N PHE A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 830 " --> pdb=" O ALA A 826 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 835 " --> pdb=" O ILE A 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 577 removed outlier: 3.737A pdb=" N TRP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 removed outlier: 3.555A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 657 Processing helix chain 'B' and resid 818 through 843 removed outlier: 4.281A pdb=" N PHE B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 583 Processing helix chain 'C' and resid 603 through 615 Processing helix chain 'C' and resid 626 through 655 Processing helix chain 'C' and resid 813 through 838 removed outlier: 4.463A pdb=" N PHE C 817 " --> pdb=" O MET C 813 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 579 Processing helix chain 'D' and resid 601 through 615 Processing helix chain 'D' and resid 627 through 654 Processing helix chain 'D' and resid 818 through 845 removed outlier: 4.139A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) 303 hydrogen bonds defined for protein. 909 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: 0.55 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 647 1.33 - 1.45: 929 1.45 - 1.57: 1988 1.57 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 3608 Sorted by residual: bond pdb=" N GLN A 556 " pdb=" CA GLN A 556 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 1.02e+01 bond pdb=" N ASN B 615 " pdb=" CA ASN B 615 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.49e+00 bond pdb=" N GLU B 552 " pdb=" CA GLU B 552 " ideal model delta sigma weight residual 1.462 1.487 -0.025 8.50e-03 1.38e+04 8.88e+00 bond pdb=" N VAL B 620 " pdb=" CA VAL B 620 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.17e-02 7.31e+03 8.50e+00 bond pdb=" N VAL C 575 " pdb=" CA VAL C 575 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.36e+00 ... (remaining 3603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 4293 1.42 - 2.84: 538 2.84 - 4.26: 96 4.26 - 5.68: 15 5.68 - 7.10: 3 Bond angle restraints: 4945 Sorted by residual: angle pdb=" N ALA B 549 " pdb=" CA ALA B 549 " pdb=" C ALA B 549 " ideal model delta sigma weight residual 112.92 108.00 4.92 1.23e+00 6.61e-01 1.60e+01 angle pdb=" N ASP C 581 " pdb=" CA ASP C 581 " pdb=" C ASP C 581 " ideal model delta sigma weight residual 111.82 107.54 4.28 1.16e+00 7.43e-01 1.36e+01 angle pdb=" CA VAL C 566 " pdb=" C VAL C 566 " pdb=" O VAL C 566 " ideal model delta sigma weight residual 120.85 116.95 3.90 1.06e+00 8.90e-01 1.36e+01 angle pdb=" N SER D 548 " pdb=" CA SER D 548 " pdb=" C SER D 548 " ideal model delta sigma weight residual 112.72 108.69 4.03 1.14e+00 7.69e-01 1.25e+01 angle pdb=" CA PHE C 810 " pdb=" C PHE C 810 " pdb=" O PHE C 810 " ideal model delta sigma weight residual 121.44 117.63 3.81 1.08e+00 8.57e-01 1.25e+01 ... (remaining 4940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.48: 1796 13.48 - 26.96: 161 26.96 - 40.44: 54 40.44 - 53.92: 12 53.92 - 67.40: 2 Dihedral angle restraints: 2025 sinusoidal: 558 harmonic: 1467 Sorted by residual: dihedral pdb=" CA ASN D 615 " pdb=" C ASN D 615 " pdb=" N ASN D 616 " pdb=" CA ASN D 616 " ideal model delta harmonic sigma weight residual -180.00 -158.66 -21.34 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA PHE D 614 " pdb=" C PHE D 614 " pdb=" N ASN D 615 " pdb=" CA ASN D 615 " ideal model delta harmonic sigma weight residual 180.00 159.99 20.01 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA MET A 576 " pdb=" C MET A 576 " pdb=" N LEU A 577 " pdb=" CA LEU A 577 " ideal model delta harmonic sigma weight residual 180.00 162.66 17.34 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 2022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 414 0.047 - 0.094: 134 0.094 - 0.141: 44 0.141 - 0.188: 21 0.188 - 0.235: 9 Chirality restraints: 622 Sorted by residual: chirality pdb=" CA VAL C 570 " pdb=" N VAL C 570 " pdb=" C VAL C 570 " pdb=" CB VAL C 570 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ASN B 615 " pdb=" N ASN B 615 " pdb=" C ASN B 615 " pdb=" CB ASN B 615 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA LEU C 577 " pdb=" N LEU C 577 " pdb=" C LEU C 577 " pdb=" CB LEU C 577 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 619 not shown) Planarity restraints: 599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 559 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C GLN C 559 " 0.034 2.00e-02 2.50e+03 pdb=" O GLN C 559 " -0.013 2.00e-02 2.50e+03 pdb=" N SER C 560 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 615 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.46e+00 pdb=" CG ASN D 615 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN D 615 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN D 615 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 578 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" C TYR C 578 " -0.026 2.00e-02 2.50e+03 pdb=" O TYR C 578 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU C 579 " 0.009 2.00e-02 2.50e+03 ... (remaining 596 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 446 2.75 - 3.29: 3881 3.29 - 3.83: 6117 3.83 - 4.36: 6469 4.36 - 4.90: 11248 Nonbonded interactions: 28161 Sorted by model distance: nonbonded pdb=" O SER A 604 " pdb=" CD1 TRP A 608 " model vdw 2.215 3.260 nonbonded pdb=" OE1 GLN C 559 " pdb=" OG1 THR C 561 " model vdw 2.242 3.040 nonbonded pdb=" O ASN B 615 " pdb=" N SER B 617 " model vdw 2.298 3.120 nonbonded pdb=" O PHE B 550 " pdb=" OH TYR B 646 " model vdw 2.307 3.040 nonbonded pdb=" O PHE A 554 " pdb=" OH TYR A 647 " model vdw 2.345 3.040 ... (remaining 28156 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 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 549 and (name N or name CA or name C or name O or name CB \ )) or resid 550 through 581 or (resid 582 and (name N or name CA or name C or n \ ame O or name CB )) or resid 583 through 832 or (resid 833 through 838 and (name \ N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 549 through 551 or (resid 552 through 553 and (name N or n \ ame CA or name C or name O or name CB )) or resid 554 or (resid 555 through 556 \ and (name N or name CA or name C or name O or name CB )) or resid 557 through 55 \ 8 or (resid 559 and (name N or name CA or name C or name O or name CB )) or resi \ d 560 through 575 or (resid 576 and (name N or name CA or name C or name O or na \ me CB )) or resid 577 or (resid 578 and (name N or name CA or name C or name O o \ r name CB )) or resid 579 or (resid 580 through 582 and (name N or name CA or na \ me C or name O or name CB )) or resid 583 through 602 or (resid 603 through 607 \ and (name N or name CA or name C or name O or name CB )) or resid 608 through 62 \ 7 or (resid 628 through 629 and (name N or name CA or name C or name O or name C \ B )) or resid 630 or (resid 631 and (name N or name CA or name C or name O or na \ me CB )) or resid 632 through 811 or (resid 812 and (name N or name CA or name C \ or name O or name CB )) or resid 813 through 824 or (resid 825 through 826 and \ (name N or name CA or name C or name O or name CB )) or resid 827 or (resid 828 \ through 838 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'B' and (resid 546 through 571 or (resid 572 through 573 and (name N or n \ ame CA or name C or name O or name CB )) or resid 574 through 577 or (resid 578 \ through 599 and (name N or name CA or name C or name O or name CB )) or resid 60 \ 0 through 811 or (resid 812 and (name N or name CA or name C or name O or name C \ B )) or resid 813 through 835 or (resid 836 and (name N or name CA or name C or \ name O or name CB )) or resid 837 through 845)) selection = (chain 'D' and ((resid 546 and (name N or name CA or name C or name O or name CB \ )) or resid 547 through 576 or (resid 577 through 599 and (name N or name CA or \ name C or name O or name CB )) or resid 600 or (resid 601 through 602 and (name \ N or name CA or name C or name O or name CB )) or resid 603 through 617 or (res \ id 618 and (name N or name CA or name C or name O or name CB )) or resid 619 thr \ ough 630 or (resid 631 and (name N or name CA or name C or name O or name CB )) \ or resid 632 through 830 or (resid 831 and (name N or name CA or name C or name \ O or name CB )) or resid 832 through 834 or (resid 835 through 836 and (name N o \ r name CA or name C or name O or name CB )) or resid 837 through 845)) } 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 group one per residue 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: 9.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.700 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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 : 0.007 0.040 3608 Z= 0.517 Angle : 0.999 7.100 4945 Z= 0.737 Chirality : 0.061 0.235 622 Planarity : 0.004 0.036 599 Dihedral : 12.870 67.400 1065 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.94 % Favored : 93.65 % Rotamer: Outliers : 0.65 % Allowed : 11.76 % Favored : 87.58 % 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: -0.15 (0.36), residues: 488 helix: 0.74 (0.25), residues: 378 sheet: None (None), residues: 0 loop : -3.02 (0.50), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 630 TYR 0.010 0.001 TYR B 823 PHE 0.019 0.002 PHE D 614 TRP 0.020 0.002 TRP C 563 HIS 0.002 0.001 HIS C 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00704 / 0.52 ( 3608) covalent geometry : angle 0.99930 / 0.74 ( 4945) hydrogen bonds : bond 0.12171 / 7.69 ( 303) hydrogen bonds : angle 5.73238 / 4.25 ( 909) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 0.134 Fit side-chains REVERT: A 813 MET cc_start: 0.5680 (mtp) cc_final: 0.5467 (mtp) REVERT: A 833 ILE cc_start: 0.7024 (tt) cc_final: 0.6788 (tt) REVERT: C 604 SER cc_start: 0.8921 (p) cc_final: 0.8664 (t) REVERT: D 562 MET cc_start: 0.7937 (tmm) cc_final: 0.7420 (tmm) outliers start: 2 outliers final: 0 residues processed: 122 average time/residue: 0.0332 time to fit residues: 5.8731 Evaluate side-chains 97 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 616 ASN B 615 ASN B 616 ASN B 649 ASN C 616 ASN C 650 ASN D 615 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.173884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.150841 restraints weight = 5473.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.154196 restraints weight = 3582.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.156280 restraints weight = 2670.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.158222 restraints weight = 2200.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.159306 restraints weight = 1883.106| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3608 Z= 0.154 Angle : 0.542 6.551 4945 Z= 0.287 Chirality : 0.038 0.218 622 Planarity : 0.004 0.027 599 Dihedral : 4.227 20.439 510 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.92 % Favored : 94.88 % Rotamer: Outliers : 4.90 % Allowed : 17.32 % Favored : 77.78 % 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: 1.31 (0.37), residues: 488 helix: 1.65 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -2.17 (0.55), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 630 TYR 0.014 0.001 TYR B 646 PHE 0.026 0.002 PHE D 614 TRP 0.012 0.001 TRP D 610 HIS 0.002 0.001 HIS C 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 3608) covalent geometry : angle 0.54219 / 0.29 ( 4945) hydrogen bonds : bond 0.04936 / 3.38 ( 303) hydrogen bonds : angle 4.11327 / 3.10 ( 909) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.128 Fit side-chains REVERT: A 833 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.7117 (tt) REVERT: B 655 ILE cc_start: 0.8656 (mt) cc_final: 0.8428 (mt) REVERT: C 604 SER cc_start: 0.8919 (p) cc_final: 0.8671 (t) REVERT: D 562 MET cc_start: 0.7945 (tmm) cc_final: 0.7466 (tmm) outliers start: 15 outliers final: 9 residues processed: 105 average time/residue: 0.0328 time to fit residues: 5.0248 Evaluate side-chains 101 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 615 ASN Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 557 ASP Chi-restraints excluded: chain D residue 838 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.0470 chunk 4 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 615 ASN B 616 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.174538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.152278 restraints weight = 5350.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.155439 restraints weight = 3574.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.157806 restraints weight = 2696.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.158856 restraints weight = 2195.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.160309 restraints weight = 1952.702| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3608 Z= 0.134 Angle : 0.511 6.958 4945 Z= 0.262 Chirality : 0.036 0.123 622 Planarity : 0.003 0.025 599 Dihedral : 3.901 17.489 510 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.71 % Favored : 95.08 % Rotamer: Outliers : 5.88 % Allowed : 17.97 % Favored : 76.14 % 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: 1.86 (0.37), residues: 488 helix: 2.07 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -2.11 (0.54), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 630 TYR 0.010 0.001 TYR B 646 PHE 0.020 0.001 PHE D 614 TRP 0.009 0.001 TRP D 607 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 3608) covalent geometry : angle 0.51120 / 0.26 ( 4945) hydrogen bonds : bond 0.04589 / 3.16 ( 303) hydrogen bonds : angle 3.81373 / 2.86 ( 909) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.139 Fit side-chains REVERT: B 655 ILE cc_start: 0.8616 (mt) cc_final: 0.8362 (mt) REVERT: D 562 MET cc_start: 0.7852 (tmm) cc_final: 0.7349 (tmm) REVERT: D 655 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8348 (mp) outliers start: 18 outliers final: 8 residues processed: 104 average time/residue: 0.0351 time to fit residues: 5.2047 Evaluate side-chains 99 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 615 ASN Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 557 ASP Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 838 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 615 ASN B 649 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.174178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.150841 restraints weight = 5439.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.154218 restraints weight = 3598.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.156269 restraints weight = 2725.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.158090 restraints weight = 2263.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.159034 restraints weight = 1968.521| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3608 Z= 0.157 Angle : 0.525 7.271 4945 Z= 0.269 Chirality : 0.037 0.123 622 Planarity : 0.003 0.026 599 Dihedral : 3.868 16.835 510 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.51 % Favored : 95.29 % Rotamer: Outliers : 5.56 % Allowed : 18.30 % Favored : 76.14 % 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: 1.98 (0.37), residues: 488 helix: 2.15 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -2.05 (0.54), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 630 TYR 0.010 0.001 TYR B 646 PHE 0.019 0.001 PHE A 554 TRP 0.009 0.001 TRP C 563 HIS 0.003 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 3608) covalent geometry : angle 0.52515 / 0.27 ( 4945) hydrogen bonds : bond 0.04623 / 3.19 ( 303) hydrogen bonds : angle 3.79841 / 2.85 ( 909) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.126 Fit side-chains REVERT: A 833 ILE cc_start: 0.7296 (OUTLIER) cc_final: 0.7039 (mm) REVERT: B 655 ILE cc_start: 0.8709 (mt) cc_final: 0.8448 (mt) REVERT: B 824 MET cc_start: 0.7975 (ttp) cc_final: 0.6290 (tpp) REVERT: D 562 MET cc_start: 0.7870 (tmm) cc_final: 0.7354 (tmm) REVERT: D 631 MET cc_start: 0.7436 (tpp) cc_final: 0.7141 (tpp) REVERT: D 655 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8311 (mp) outliers start: 17 outliers final: 11 residues processed: 100 average time/residue: 0.0335 time to fit residues: 4.8910 Evaluate side-chains 104 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 615 ASN Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 557 ASP Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 838 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 615 ASN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.176014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.152786 restraints weight = 5473.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.156061 restraints weight = 3612.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.158557 restraints weight = 2720.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.159557 restraints weight = 2202.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.161057 restraints weight = 1977.858| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3608 Z= 0.126 Angle : 0.483 6.036 4945 Z= 0.251 Chirality : 0.036 0.123 622 Planarity : 0.003 0.025 599 Dihedral : 3.639 13.312 510 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.10 % Favored : 95.49 % Rotamer: Outliers : 4.58 % Allowed : 20.92 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.30 (0.37), residues: 488 helix: 2.39 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -2.01 (0.55), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 630 TYR 0.007 0.001 TYR B 646 PHE 0.013 0.001 PHE D 614 TRP 0.012 0.001 TRP D 607 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 3608) covalent geometry : angle 0.48301 / 0.25 ( 4945) hydrogen bonds : bond 0.04300 / 2.95 ( 303) hydrogen bonds : angle 3.66206 / 2.74 ( 909) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.126 Fit side-chains REVERT: A 582 ARG cc_start: 0.7705 (ptt180) cc_final: 0.7370 (ptp90) REVERT: A 833 ILE cc_start: 0.7241 (OUTLIER) cc_final: 0.7010 (mm) REVERT: B 655 ILE cc_start: 0.8713 (mt) cc_final: 0.8430 (mt) REVERT: B 824 MET cc_start: 0.7903 (ttp) cc_final: 0.6286 (tpp) REVERT: D 562 MET cc_start: 0.7874 (tmm) cc_final: 0.7378 (tmm) REVERT: D 655 ILE cc_start: 0.8519 (mt) cc_final: 0.8281 (mp) outliers start: 14 outliers final: 9 residues processed: 104 average time/residue: 0.0370 time to fit residues: 5.3398 Evaluate side-chains 102 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 557 ASP Chi-restraints excluded: chain D residue 617 SER Chi-restraints excluded: chain D residue 838 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 26 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 7 optimal weight: 0.0980 chunk 24 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 649 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.175485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.152734 restraints weight = 5428.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.155970 restraints weight = 3495.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.158347 restraints weight = 2612.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.159851 restraints weight = 2115.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.161104 restraints weight = 1831.592| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3608 Z= 0.123 Angle : 0.496 7.333 4945 Z= 0.247 Chirality : 0.036 0.132 622 Planarity : 0.003 0.025 599 Dihedral : 3.583 12.996 510 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.69 % Favored : 96.11 % Rotamer: Outliers : 5.23 % Allowed : 18.95 % Favored : 75.82 % 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: 2.52 (0.38), residues: 488 helix: 2.48 (0.25), residues: 388 sheet: None (None), residues: 0 loop : -1.78 (0.58), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 630 TYR 0.006 0.001 TYR B 646 PHE 0.016 0.001 PHE A 554 TRP 0.012 0.001 TRP D 607 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 3608) covalent geometry : angle 0.49612 / 0.25 ( 4945) hydrogen bonds : bond 0.04161 / 2.85 ( 303) hydrogen bonds : angle 3.55588 / 2.66 ( 909) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.133 Fit side-chains REVERT: A 582 ARG cc_start: 0.7599 (ptt180) cc_final: 0.7339 (ptp90) REVERT: A 833 ILE cc_start: 0.7236 (OUTLIER) cc_final: 0.7020 (mm) REVERT: B 655 ILE cc_start: 0.8724 (mt) cc_final: 0.8450 (mt) REVERT: B 824 MET cc_start: 0.7667 (ttp) cc_final: 0.5462 (mmp) REVERT: D 562 MET cc_start: 0.7847 (tmm) cc_final: 0.7349 (tmm) REVERT: D 655 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8293 (mp) outliers start: 16 outliers final: 11 residues processed: 100 average time/residue: 0.0382 time to fit residues: 5.4011 Evaluate side-chains 102 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 557 ASP Chi-restraints excluded: chain D residue 617 SER Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 838 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.174694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.150925 restraints weight = 5582.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.154115 restraints weight = 3719.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.156368 restraints weight = 2837.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.157787 restraints weight = 2345.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.158902 restraints weight = 2056.389| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3608 Z= 0.168 Angle : 0.553 8.529 4945 Z= 0.276 Chirality : 0.038 0.157 622 Planarity : 0.003 0.028 599 Dihedral : 3.792 14.257 510 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.71 % Favored : 95.08 % Rotamer: Outliers : 5.23 % Allowed : 20.26 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.30 (0.37), residues: 488 helix: 2.32 (0.25), residues: 388 sheet: None (None), residues: 0 loop : -1.87 (0.58), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 630 TYR 0.007 0.001 TYR B 646 PHE 0.013 0.001 PHE D 614 TRP 0.010 0.001 TRP B 635 HIS 0.003 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 3608) covalent geometry : angle 0.55273 / 0.28 ( 4945) hydrogen bonds : bond 0.04655 / 3.19 ( 303) hydrogen bonds : angle 3.74545 / 2.81 ( 909) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.133 Fit side-chains REVERT: A 582 ARG cc_start: 0.7709 (ptt180) cc_final: 0.7302 (ptt-90) REVERT: A 833 ILE cc_start: 0.7232 (OUTLIER) cc_final: 0.6988 (mm) REVERT: B 655 ILE cc_start: 0.8754 (mt) cc_final: 0.8496 (mt) REVERT: B 824 MET cc_start: 0.7787 (ttp) cc_final: 0.5528 (mmp) REVERT: D 562 MET cc_start: 0.7914 (tmm) cc_final: 0.7414 (tmm) REVERT: D 655 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8281 (mp) outliers start: 16 outliers final: 13 residues processed: 99 average time/residue: 0.0403 time to fit residues: 5.6982 Evaluate side-chains 102 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 557 ASP Chi-restraints excluded: chain D residue 617 SER Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 815 ILE Chi-restraints excluded: chain D residue 838 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.0000 chunk 36 optimal weight: 0.6980 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.177239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.153555 restraints weight = 5568.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.156800 restraints weight = 3690.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.158830 restraints weight = 2788.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.160690 restraints weight = 2315.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.161646 restraints weight = 1996.192| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3608 Z= 0.135 Angle : 0.535 10.013 4945 Z= 0.266 Chirality : 0.037 0.216 622 Planarity : 0.003 0.027 599 Dihedral : 3.653 13.426 510 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.89 % Favored : 95.90 % Rotamer: Outliers : 4.90 % Allowed : 20.92 % Favored : 74.18 % 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: 2.39 (0.38), residues: 488 helix: 2.38 (0.25), residues: 388 sheet: None (None), residues: 0 loop : -1.81 (0.58), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 630 TYR 0.006 0.001 TYR B 646 PHE 0.021 0.001 PHE B 600 TRP 0.010 0.001 TRP D 607 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 3608) covalent geometry : angle 0.53510 / 0.27 ( 4945) hydrogen bonds : bond 0.04256 / 2.90 ( 303) hydrogen bonds : angle 3.65304 / 2.74 ( 909) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.128 Fit side-chains REVERT: A 582 ARG cc_start: 0.7632 (ptt180) cc_final: 0.7399 (ptt-90) REVERT: B 655 ILE cc_start: 0.8730 (mt) cc_final: 0.8460 (mt) REVERT: B 824 MET cc_start: 0.7622 (ttp) cc_final: 0.5408 (mmp) REVERT: D 562 MET cc_start: 0.7892 (tmm) cc_final: 0.7411 (tmm) REVERT: D 655 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8186 (mp) outliers start: 15 outliers final: 12 residues processed: 103 average time/residue: 0.0351 time to fit residues: 5.1515 Evaluate side-chains 107 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 557 ASP Chi-restraints excluded: chain D residue 617 SER Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 815 ILE Chi-restraints excluded: chain D residue 838 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 0.0670 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 649 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.178153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.154879 restraints weight = 5445.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.158079 restraints weight = 3561.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.160393 restraints weight = 2690.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.162014 restraints weight = 2204.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.162823 restraints weight = 1904.139| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3608 Z= 0.132 Angle : 0.544 11.524 4945 Z= 0.267 Chirality : 0.038 0.272 622 Planarity : 0.003 0.027 599 Dihedral : 3.588 12.713 510 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.10 % Favored : 95.70 % Rotamer: Outliers : 4.90 % Allowed : 21.24 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.46 (0.38), residues: 488 helix: 2.45 (0.25), residues: 388 sheet: None (None), residues: 0 loop : -1.85 (0.58), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 630 TYR 0.006 0.001 TYR B 646 PHE 0.017 0.001 PHE A 554 TRP 0.009 0.001 TRP D 607 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 3608) covalent geometry : angle 0.54385 / 0.27 ( 4945) hydrogen bonds : bond 0.04214 / 2.87 ( 303) hydrogen bonds : angle 3.60757 / 2.71 ( 909) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.159 Fit side-chains REVERT: A 582 ARG cc_start: 0.7642 (ptt180) cc_final: 0.7393 (ptt-90) REVERT: B 655 ILE cc_start: 0.8739 (mt) cc_final: 0.8464 (mt) REVERT: B 824 MET cc_start: 0.7535 (ttp) cc_final: 0.5317 (mmp) REVERT: D 562 MET cc_start: 0.7858 (tmm) cc_final: 0.7373 (tmm) REVERT: D 655 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8174 (mp) outliers start: 15 outliers final: 11 residues processed: 100 average time/residue: 0.0389 time to fit residues: 5.4758 Evaluate side-chains 102 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 557 ASP Chi-restraints excluded: chain D residue 617 SER Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 838 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 6 optimal weight: 0.0870 chunk 34 optimal weight: 0.0670 chunk 43 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.0980 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.0000 chunk 47 optimal weight: 0.8980 overall best weight: 0.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 649 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.178724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.154967 restraints weight = 5506.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.158200 restraints weight = 3610.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.160496 restraints weight = 2723.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.161625 restraints weight = 2245.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.162802 restraints weight = 2002.643| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3608 Z= 0.107 Angle : 0.538 11.567 4945 Z= 0.254 Chirality : 0.037 0.282 622 Planarity : 0.003 0.026 599 Dihedral : 3.379 12.782 510 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.69 % Favored : 96.11 % Rotamer: Outliers : 3.59 % Allowed : 22.88 % Favored : 73.53 % 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: 2.74 (0.38), residues: 488 helix: 2.72 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -1.94 (0.57), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 630 TYR 0.005 0.001 TYR D 646 PHE 0.022 0.001 PHE A 654 TRP 0.011 0.001 TRP D 607 HIS 0.001 0.000 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.11 ( 3608) covalent geometry : angle 0.53760 / 0.25 ( 4945) hydrogen bonds : bond 0.03657 / 2.48 ( 303) hydrogen bonds : angle 3.43954 / 2.58 ( 909) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.132 Fit side-chains REVERT: B 655 ILE cc_start: 0.8748 (mt) cc_final: 0.8465 (mt) REVERT: B 824 MET cc_start: 0.7300 (ttp) cc_final: 0.4955 (mmp) REVERT: D 562 MET cc_start: 0.7816 (tmm) cc_final: 0.7559 (tmm) REVERT: D 645 SER cc_start: 0.9026 (m) cc_final: 0.8730 (m) outliers start: 11 outliers final: 4 residues processed: 100 average time/residue: 0.0347 time to fit residues: 4.8807 Evaluate side-chains 93 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain D residue 617 SER Chi-restraints excluded: chain D residue 838 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 42 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.174768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.150911 restraints weight = 5496.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.154045 restraints weight = 3694.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.156301 restraints weight = 2831.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.157617 restraints weight = 2348.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.158808 restraints weight = 2080.672| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3608 Z= 0.137 Angle : 0.574 11.949 4945 Z= 0.278 Chirality : 0.038 0.289 622 Planarity : 0.003 0.027 599 Dihedral : 3.455 11.852 510 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.10 % Favored : 95.70 % Rotamer: Outliers : 1.63 % Allowed : 25.49 % Favored : 72.88 % 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: 2.65 (0.38), residues: 488 helix: 2.73 (0.25), residues: 382 sheet: None (None), residues: 0 loop : -2.19 (0.56), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 630 TYR 0.005 0.001 TYR B 646 PHE 0.017 0.001 PHE A 554 TRP 0.009 0.001 TRP D 559 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 3608) covalent geometry : angle 0.57435 / 0.28 ( 4945) hydrogen bonds : bond 0.04053 / 2.74 ( 303) hydrogen bonds : angle 3.59027 / 2.71 ( 909) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 888.91 seconds wall clock time: 15 minutes 58.10 seconds (958.10 seconds total)