Starting phenix.real_space_refine on Wed Jun 3 10:44:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oby_70303/06_2026/9oby_70303.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oby_70303/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9oby_70303/06_2026/9oby_70303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oby_70303/06_2026/9oby_70303.map" model { file = "/net/cci-nas-00/data/ceres_data/9oby_70303/06_2026/9oby_70303.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oby_70303/06_2026/9oby_70303.cif" } 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-6079/lib/python3.9/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 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: 0.99, per 1000 atoms: 0.28 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: 0.22 Conformation dependent library (CDL) restraints added in 129.2 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: 0.09 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: 0.51 Time building geometry restraints manager: 0.33 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: 7.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.830 Find NCS groups from input model: 0.050 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 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 : 0.101 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: 0.0316 time to fit residues: 5.6100 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 : 0.127 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 616 ASN B 616 ASN B 649 ASN C 616 ASN C 650 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.173914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.151152 restraints weight = 5454.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.154370 restraints weight = 3514.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.156731 restraints weight = 2635.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.157598 restraints weight = 2141.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.159209 restraints weight = 1933.854| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2144 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= 0.151 Angle : 0.539 6.877 4945 Z= 0.284 Chirality : 0.038 0.224 622 Planarity : 0.004 0.027 599 Dihedral : 4.157 17.259 510 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.71 % Favored : 95.08 % Rotamer: Outliers : 4.90 % Allowed : 17.97 % Favored : 77.12 % 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: 1.33 (0.37), residues: 488 helix: 1.66 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -2.15 (0.55), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 630 TYR 0.013 0.001 TYR B 646 PHE 0.025 0.002 PHE D 614 TRP 0.012 0.001 TRP B 610 HIS 0.002 0.001 HIS C 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 3608) covalent geometry : angle 0.53943 / 0.28 ( 4945) hydrogen bonds : bond 0.04921 / 3.37 ( 303) hydrogen bonds : angle 4.07895 / 3.06 ( 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 : 0.134 Fit side-chains REVERT: A 833 ILE cc_start: 0.7323 (OUTLIER) cc_final: 0.7101 (tt) REVERT: B 655 ILE cc_start: 0.8647 (mt) cc_final: 0.8415 (mt) REVERT: C 604 SER cc_start: 0.8926 (p) cc_final: 0.8683 (t) REVERT: D 562 MET cc_start: 0.7964 (tmm) cc_final: 0.7483 (tmm) outliers start: 15 outliers final: 9 residues processed: 105 average time/residue: 0.0320 time to fit residues: 4.8629 Evaluate side-chains 100 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.089 ------------------------------------------------------------------------------- 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: 0.9990 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 12 optimal weight: 0.0170 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 649 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.176029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.152967 restraints weight = 5476.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.156331 restraints weight = 3556.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.158820 restraints weight = 2671.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.160003 restraints weight = 2175.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.161164 restraints weight = 1920.052| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2428 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= 0.133 Angle : 0.504 7.335 4945 Z= 0.259 Chirality : 0.036 0.124 622 Planarity : 0.003 0.026 599 Dihedral : 3.843 14.174 510 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.71 % Favored : 95.08 % Rotamer: Outliers : 6.21 % Allowed : 17.65 % 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: 1.92 (0.37), residues: 488 helix: 2.12 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -2.10 (0.54), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 582 TYR 0.010 0.001 TYR B 646 PHE 0.019 0.001 PHE D 614 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 0.00282 / 0.13 ( 3608) covalent geometry : angle 0.50393 / 0.26 ( 4945) hydrogen bonds : bond 0.04575 / 3.14 ( 303) hydrogen bonds : angle 3.77450 / 2.83 ( 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 111 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.112 Fit side-chains REVERT: A 583 PHE cc_start: 0.7706 (m-10) cc_final: 0.7447 (m-10) REVERT: B 655 ILE cc_start: 0.8667 (mt) cc_final: 0.8424 (mt) REVERT: D 562 MET cc_start: 0.7855 (tmm) cc_final: 0.7345 (tmm) REVERT: D 629 LYS cc_start: 0.8535 (mttt) cc_final: 0.8328 (mttp) REVERT: D 655 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8379 (mp) outliers start: 19 outliers final: 11 residues processed: 102 average time/residue: 0.0331 time to fit residues: 4.8408 Evaluate side-chains 103 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.151 ------------------------------------------------------------------------------- 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 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 558 VAL Chi-restraints excluded: chain D residue 615 ASN 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: 2.9990 chunk 28 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 649 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.172958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.150078 restraints weight = 5366.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.153331 restraints weight = 3508.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.155717 restraints weight = 2632.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.157071 restraints weight = 2147.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.157895 restraints weight = 1878.615| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3608 Z= 0.164 Angle : 0.528 7.418 4945 Z= 0.272 Chirality : 0.037 0.125 622 Planarity : 0.003 0.026 599 Dihedral : 3.889 13.932 510 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.51 % Favored : 95.29 % Rotamer: Outliers : 5.88 % Allowed : 18.63 % Favored : 75.49 % 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: 1.96 (0.37), residues: 488 helix: 2.14 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -2.07 (0.55), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 630 TYR 0.009 0.001 TYR B 646 PHE 0.019 0.002 PHE A 554 TRP 0.010 0.001 TRP C 563 HIS 0.003 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 3608) covalent geometry : angle 0.52782 / 0.27 ( 4945) hydrogen bonds : bond 0.04765 / 3.26 ( 303) hydrogen bonds : angle 3.83446 / 2.88 ( 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: 18 poor density : 92 time to evaluate : 0.194 Fit side-chains REVERT: A 583 PHE cc_start: 0.7689 (m-10) cc_final: 0.7480 (m-10) REVERT: A 833 ILE cc_start: 0.7227 (OUTLIER) cc_final: 0.6976 (mm) REVERT: B 615 ASN cc_start: 0.6657 (OUTLIER) cc_final: 0.6373 (t0) REVERT: B 655 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8478 (mt) REVERT: B 824 MET cc_start: 0.7975 (ttp) cc_final: 0.6289 (tpp) REVERT: D 562 MET cc_start: 0.7880 (tmm) cc_final: 0.7381 (tmm) REVERT: D 631 MET cc_start: 0.7528 (tpp) cc_final: 0.7235 (tpp) REVERT: D 655 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8344 (mp) outliers start: 18 outliers final: 12 residues processed: 101 average time/residue: 0.0369 time to fit residues: 5.4300 Evaluate side-chains 105 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.121 ------------------------------------------------------------------------------- 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 615 ASN Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 655 ILE 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 606 ILE Chi-restraints excluded: chain D residue 618 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 2.9990 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: 0.2980 chunk 38 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 649 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.172919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.149975 restraints weight = 5428.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.153177 restraints weight = 3558.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.154990 restraints weight = 2678.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.156859 restraints weight = 2243.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.156859 restraints weight = 1948.140| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3608 Z= 0.159 Angle : 0.525 5.964 4945 Z= 0.270 Chirality : 0.037 0.132 622 Planarity : 0.003 0.027 599 Dihedral : 3.827 13.856 510 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 5.88 % Allowed : 21.90 % Favored : 72.22 % 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: 2.07 (0.37), residues: 488 helix: 2.23 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -2.06 (0.55), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 630 TYR 0.008 0.001 TYR B 646 PHE 0.015 0.001 PHE D 614 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 0.00360 / 0.16 ( 3608) covalent geometry : angle 0.52536 / 0.27 ( 4945) hydrogen bonds : bond 0.04666 / 3.19 ( 303) hydrogen bonds : angle 3.81248 / 2.86 ( 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 112 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.139 Fit side-chains REVERT: A 583 PHE cc_start: 0.7658 (m-10) cc_final: 0.7449 (m-10) REVERT: A 833 ILE cc_start: 0.7226 (OUTLIER) cc_final: 0.6987 (mm) REVERT: B 615 ASN cc_start: 0.6718 (OUTLIER) cc_final: 0.6300 (t0) REVERT: B 655 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8472 (mt) REVERT: B 824 MET cc_start: 0.7912 (ttp) cc_final: 0.6220 (tpp) REVERT: D 562 MET cc_start: 0.7884 (tmm) cc_final: 0.7384 (tmm) REVERT: D 655 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8320 (mp) outliers start: 18 outliers final: 14 residues processed: 104 average time/residue: 0.0361 time to fit residues: 5.3955 Evaluate side-chains 109 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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 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 B residue 655 ILE 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 606 ILE Chi-restraints excluded: chain D residue 617 SER Chi-restraints excluded: chain D residue 618 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.174399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.151504 restraints weight = 5438.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.154689 restraints weight = 3554.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.156694 restraints weight = 2673.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.158521 restraints weight = 2215.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.159052 restraints weight = 1910.036| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3608 Z= 0.134 Angle : 0.503 6.156 4945 Z= 0.257 Chirality : 0.036 0.138 622 Planarity : 0.003 0.027 599 Dihedral : 3.700 12.759 510 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.10 % Favored : 95.70 % Rotamer: Outliers : 5.88 % Allowed : 21.24 % 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: 2.23 (0.37), residues: 488 helix: 2.30 (0.25), residues: 388 sheet: None (None), residues: 0 loop : -2.00 (0.56), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 630 TYR 0.006 0.001 TYR B 646 PHE 0.015 0.001 PHE D 614 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 0.00296 / 0.13 ( 3608) covalent geometry : angle 0.50331 / 0.26 ( 4945) hydrogen bonds : bond 0.04397 / 3.00 ( 303) hydrogen bonds : angle 3.71818 / 2.78 ( 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 113 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.128 Fit side-chains REVERT: A 833 ILE cc_start: 0.7224 (OUTLIER) cc_final: 0.7015 (mm) REVERT: B 655 ILE cc_start: 0.8711 (mt) cc_final: 0.8441 (mt) REVERT: B 824 MET cc_start: 0.7766 (ttp) cc_final: 0.5627 (mmt) REVERT: D 562 MET cc_start: 0.7840 (tmm) cc_final: 0.7332 (tmm) REVERT: D 655 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8250 (mp) outliers start: 18 outliers final: 12 residues processed: 105 average time/residue: 0.0341 time to fit residues: 5.1413 Evaluate side-chains 104 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 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 615 ASN 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: 0.9980 chunk 18 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 649 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.174082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.150395 restraints weight = 5585.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.153649 restraints weight = 3677.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.155936 restraints weight = 2791.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.157272 restraints weight = 2306.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.158628 restraints weight = 2034.633| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3608 Z= 0.156 Angle : 0.538 7.343 4945 Z= 0.274 Chirality : 0.038 0.143 622 Planarity : 0.003 0.030 599 Dihedral : 3.785 13.723 510 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.51 % Favored : 95.29 % Rotamer: Outliers : 7.52 % Allowed : 19.93 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.18 (0.37), residues: 488 helix: 2.31 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -2.06 (0.56), residues: 104 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 0.015 0.001 PHE D 614 TRP 0.010 0.001 TRP C 563 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 3608) covalent geometry : angle 0.53750 / 0.27 ( 4945) hydrogen bonds : bond 0.04586 / 3.12 ( 303) hydrogen bonds : angle 3.78175 / 2.83 ( 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 113 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.128 Fit side-chains REVERT: A 833 ILE cc_start: 0.7221 (OUTLIER) cc_final: 0.7004 (mm) REVERT: B 655 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8464 (mt) REVERT: B 824 MET cc_start: 0.7754 (ttp) cc_final: 0.5572 (mmp) REVERT: D 562 MET cc_start: 0.7872 (tmm) cc_final: 0.7375 (tmm) REVERT: D 655 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8276 (mp) outliers start: 23 outliers final: 15 residues processed: 103 average time/residue: 0.0334 time to fit residues: 5.0554 Evaluate side-chains 106 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 562 LEU 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 655 ILE 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 606 ILE Chi-restraints excluded: chain D residue 617 SER Chi-restraints excluded: chain D residue 618 VAL 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: 3.9990 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 5 optimal weight: 0.0170 chunk 25 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.178695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.155905 restraints weight = 5562.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.158858 restraints weight = 3781.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.161018 restraints weight = 2930.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.162102 restraints weight = 2442.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.163359 restraints weight = 2181.896| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3608 Z= 0.128 Angle : 0.533 9.600 4945 Z= 0.263 Chirality : 0.037 0.218 622 Planarity : 0.003 0.028 599 Dihedral : 3.588 12.711 510 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.30 % Favored : 95.49 % Rotamer: Outliers : 6.21 % Allowed : 20.92 % 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: 2.39 (0.38), residues: 488 helix: 2.44 (0.25), residues: 386 sheet: None (None), residues: 0 loop : -2.00 (0.57), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 630 TYR 0.005 0.001 TYR B 646 PHE 0.010 0.001 PHE A 639 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 0.00283 / 0.13 ( 3608) covalent geometry : angle 0.53294 / 0.26 ( 4945) hydrogen bonds : bond 0.04156 / 2.82 ( 303) hydrogen bonds : angle 3.67108 / 2.75 ( 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 112 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.138 Fit side-chains REVERT: A 582 ARG cc_start: 0.7604 (ptt180) cc_final: 0.7280 (ptt-90) REVERT: A 583 PHE cc_start: 0.7480 (m-10) cc_final: 0.7253 (m-10) REVERT: B 655 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8422 (mt) REVERT: B 824 MET cc_start: 0.7497 (ttp) cc_final: 0.5357 (mmp) REVERT: D 562 MET cc_start: 0.7745 (tmm) cc_final: 0.7248 (tmm) REVERT: D 655 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8149 (mp) outliers start: 19 outliers final: 13 residues processed: 104 average time/residue: 0.0398 time to fit residues: 5.7379 Evaluate side-chains 105 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 655 ILE 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 606 ILE Chi-restraints excluded: chain D residue 615 ASN 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: 4.9990 chunk 32 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 25 optimal weight: 0.0980 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 30 optimal weight: 0.0000 chunk 27 optimal weight: 0.6980 overall best weight: 0.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.177839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.153546 restraints weight = 5446.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.156742 restraints weight = 3672.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.158828 restraints weight = 2828.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.160548 restraints weight = 2371.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.161504 restraints weight = 2073.469| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 3608 Z= 0.116 Angle : 0.535 10.910 4945 Z= 0.260 Chirality : 0.037 0.268 622 Planarity : 0.003 0.027 599 Dihedral : 3.419 12.071 510 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.30 % Favored : 95.49 % Rotamer: Outliers : 4.25 % Allowed : 23.53 % Favored : 72.22 % 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: 2.59 (0.38), residues: 488 helix: 2.63 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -2.01 (0.57), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 630 TYR 0.004 0.001 TYR B 646 PHE 0.009 0.001 PHE A 639 TRP 0.012 0.001 TRP D 607 HIS 0.001 0.000 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 ( 3608) covalent geometry : angle 0.53514 / 0.26 ( 4945) hydrogen bonds : bond 0.03971 / 2.69 ( 303) hydrogen bonds : angle 3.55659 / 2.67 ( 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 101 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.154 Fit side-chains REVERT: A 582 ARG cc_start: 0.7593 (ptt180) cc_final: 0.7197 (ptt-90) REVERT: A 583 PHE cc_start: 0.7421 (m-10) cc_final: 0.7162 (m-10) REVERT: B 655 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8460 (mt) REVERT: B 824 MET cc_start: 0.7362 (ttp) cc_final: 0.5034 (mmp) REVERT: D 562 MET cc_start: 0.7775 (tmm) cc_final: 0.7484 (tmm) REVERT: D 631 MET cc_start: 0.7513 (tpp) cc_final: 0.7146 (tpp) outliers start: 13 outliers final: 10 residues processed: 95 average time/residue: 0.0389 time to fit residues: 5.2574 Evaluate side-chains 98 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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 622 ASN Chi-restraints excluded: chain B residue 655 ILE 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 615 ASN 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 6 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 0.0670 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.174476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.150200 restraints weight = 5546.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.153494 restraints weight = 3686.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.155723 restraints weight = 2798.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.156968 restraints weight = 2317.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.158336 restraints weight = 2054.165| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3608 Z= 0.135 Angle : 0.562 11.783 4945 Z= 0.272 Chirality : 0.038 0.276 622 Planarity : 0.003 0.027 599 Dihedral : 3.517 14.192 510 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.10 % Favored : 95.70 % Rotamer: Outliers : 4.90 % Allowed : 22.88 % Favored : 72.22 % 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: 2.54 (0.38), residues: 488 helix: 2.59 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -2.04 (0.57), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 582 TYR 0.005 0.001 TYR B 646 PHE 0.021 0.001 PHE A 654 TRP 0.014 0.001 TRP D 607 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 3608) covalent geometry : angle 0.56205 / 0.27 ( 4945) hydrogen bonds : bond 0.04190 / 2.83 ( 303) hydrogen bonds : angle 3.64330 / 2.74 ( 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 99 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.126 Fit side-chains REVERT: B 655 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8494 (mt) REVERT: B 824 MET cc_start: 0.7408 (ttp) cc_final: 0.5162 (mmp) REVERT: D 562 MET cc_start: 0.7861 (tmm) cc_final: 0.7578 (tmm) REVERT: D 631 MET cc_start: 0.7546 (tpp) cc_final: 0.7171 (tpp) REVERT: D 655 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8194 (mp) outliers start: 15 outliers final: 11 residues processed: 94 average time/residue: 0.0335 time to fit residues: 4.6196 Evaluate side-chains 96 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 622 ASN Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 557 ASP Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 615 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 3 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 0.0370 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.175102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.150756 restraints weight = 5356.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.153980 restraints weight = 3590.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.156177 restraints weight = 2737.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.157524 restraints weight = 2278.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.158267 restraints weight = 2014.016| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3608 Z= 0.131 Angle : 0.559 12.285 4945 Z= 0.270 Chirality : 0.038 0.297 622 Planarity : 0.003 0.027 599 Dihedral : 3.449 13.168 510 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.30 % Favored : 95.49 % Rotamer: Outliers : 4.90 % Allowed : 23.53 % Favored : 71.57 % 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: 2.61 (0.38), residues: 488 helix: 2.74 (0.25), residues: 381 sheet: None (None), residues: 0 loop : -2.33 (0.55), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 630 TYR 0.004 0.001 TYR D 646 PHE 0.008 0.001 PHE A 639 TRP 0.008 0.001 TRP D 607 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 3608) covalent geometry : angle 0.55905 / 0.27 ( 4945) hydrogen bonds : bond 0.04095 / 2.77 ( 303) hydrogen bonds : angle 3.63938 / 2.75 ( 909) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 859.47 seconds wall clock time: 15 minutes 48.06 seconds (948.06 seconds total)