Starting phenix.real_space_refine on Fri Dec 27 09:33:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eqs_28544/12_2024/8eqs_28544_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eqs_28544/12_2024/8eqs_28544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eqs_28544/12_2024/8eqs_28544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eqs_28544/12_2024/8eqs_28544.map" model { file = "/net/cci-nas-00/data/ceres_data/8eqs_28544/12_2024/8eqs_28544_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eqs_28544/12_2024/8eqs_28544_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 20 5.16 5 C 2406 2.51 5 N 570 2.21 5 O 656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3654 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1573 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 3, 'TRANS': 188} Chain breaks: 1 Chain: "C" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 229 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Restraints were copied for chains: D, B Time building chain proxies: 2.93, per 1000 atoms: 0.80 Number of scatterers: 3654 At special positions: 0 Unit cell: (73.428, 64.988, 89.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 2 15.00 O 656 8.00 N 570 7.00 C 2406 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: 0.98 Conformation dependent library (CDL) restraints added in 1.1 seconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 2 sheets defined 53.9% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 43 through 61 removed outlier: 3.553A pdb=" N VAL A 47 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 100 removed outlier: 3.600A pdb=" N LEU A 71 " --> pdb=" O LYS A 67 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 72 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 134 Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'B' and resid 43 through 61 removed outlier: 3.553A pdb=" N VAL B 47 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 100 removed outlier: 3.600A pdb=" N LEU B 71 " --> pdb=" O LYS B 67 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 78 " --> pdb=" O TYR B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 134 Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'C' and resid 26 through 48 Proline residue: C 34 - end of helix removed outlier: 4.378A pdb=" N GLN C 37 " --> pdb=" O GLY C 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 48 Proline residue: D 34 - end of helix removed outlier: 4.378A pdb=" N GLN D 37 " --> pdb=" O GLY D 33 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 155 through 160 removed outlier: 5.812A pdb=" N HIS A 150 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N TYR A 200 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE A 232 " --> pdb=" O GLU A 215 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR A 217 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE A 230 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 155 through 160 removed outlier: 5.812A pdb=" N HIS B 150 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N TYR B 200 " --> pdb=" O HIS B 150 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE B 232 " --> pdb=" O GLU B 215 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR B 217 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE B 230 " --> pdb=" O THR B 217 " (cutoff:3.500A) 234 hydrogen bonds defined for protein. 678 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: 0.93 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 566 1.31 - 1.44: 1140 1.44 - 1.56: 2016 1.56 - 1.69: 4 1.69 - 1.81: 24 Bond restraints: 3750 Sorted by residual: bond pdb=" C10 PEE B 401 " pdb=" O2 PEE B 401 " ideal model delta sigma weight residual 1.332 1.424 -0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C10 PEE A 401 " pdb=" O2 PEE A 401 " ideal model delta sigma weight residual 1.332 1.423 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C30 PEE A 401 " pdb=" O3 PEE A 401 " ideal model delta sigma weight residual 1.327 1.411 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C30 PEE B 401 " pdb=" O3 PEE B 401 " ideal model delta sigma weight residual 1.327 1.410 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C10 PEE A 401 " pdb=" C11 PEE A 401 " ideal model delta sigma weight residual 1.504 1.549 -0.045 2.00e-02 2.50e+03 5.17e+00 ... (remaining 3745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 5049 3.37 - 6.74: 29 6.74 - 10.11: 4 10.11 - 13.48: 2 13.48 - 16.85: 2 Bond angle restraints: 5086 Sorted by residual: angle pdb=" O3P PEE B 401 " pdb=" P PEE B 401 " pdb=" O4P PEE B 401 " ideal model delta sigma weight residual 92.91 109.76 -16.85 3.00e+00 1.11e-01 3.15e+01 angle pdb=" O3P PEE A 401 " pdb=" P PEE A 401 " pdb=" O4P PEE A 401 " ideal model delta sigma weight residual 92.91 109.76 -16.85 3.00e+00 1.11e-01 3.15e+01 angle pdb=" O1P PEE A 401 " pdb=" P PEE A 401 " pdb=" O2P PEE A 401 " ideal model delta sigma weight residual 119.43 109.24 10.19 3.00e+00 1.11e-01 1.15e+01 angle pdb=" O1P PEE B 401 " pdb=" P PEE B 401 " pdb=" O2P PEE B 401 " ideal model delta sigma weight residual 119.43 109.24 10.19 3.00e+00 1.11e-01 1.15e+01 angle pdb=" C11 PEE B 401 " pdb=" C10 PEE B 401 " pdb=" O2 PEE B 401 " ideal model delta sigma weight residual 111.70 120.37 -8.67 3.00e+00 1.11e-01 8.35e+00 ... (remaining 5081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.50: 2070 31.50 - 63.00: 58 63.00 - 94.50: 12 94.50 - 126.00: 0 126.00 - 157.50: 6 Dihedral angle restraints: 2146 sinusoidal: 858 harmonic: 1288 Sorted by residual: dihedral pdb=" C3 PEE A 401 " pdb=" C1 PEE A 401 " pdb=" C2 PEE A 401 " pdb=" O3P PEE A 401 " ideal model delta sinusoidal sigma weight residual 62.73 -94.77 157.50 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C3 PEE B 401 " pdb=" C1 PEE B 401 " pdb=" C2 PEE B 401 " pdb=" O3P PEE B 401 " ideal model delta sinusoidal sigma weight residual 62.73 -94.74 157.47 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C2 PEE A 401 " pdb=" C10 PEE A 401 " pdb=" O2 PEE A 401 " pdb=" O4 PEE A 401 " ideal model delta sinusoidal sigma weight residual 2.73 -153.71 156.44 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 2143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 485 0.063 - 0.125: 61 0.125 - 0.188: 8 0.188 - 0.251: 0 0.251 - 0.314: 2 Chirality restraints: 556 Sorted by residual: chirality pdb=" C2 PEE B 401 " pdb=" C1 PEE B 401 " pdb=" C3 PEE B 401 " pdb=" O2 PEE B 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.64 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C2 PEE A 401 " pdb=" C1 PEE A 401 " pdb=" C3 PEE A 401 " pdb=" O2 PEE A 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.64 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA ILE A 186 " pdb=" N ILE A 186 " pdb=" C ILE A 186 " pdb=" CB ILE A 186 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 553 not shown) Planarity restraints: 622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 80 " 0.007 2.00e-02 2.50e+03 1.31e-02 1.73e+00 pdb=" C ILE A 80 " -0.023 2.00e-02 2.50e+03 pdb=" O ILE A 80 " 0.009 2.00e-02 2.50e+03 pdb=" N CYS A 81 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 80 " -0.007 2.00e-02 2.50e+03 1.31e-02 1.70e+00 pdb=" C ILE B 80 " 0.023 2.00e-02 2.50e+03 pdb=" O ILE B 80 " -0.009 2.00e-02 2.50e+03 pdb=" N CYS B 81 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 82 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.66e+00 pdb=" C ASN A 82 " 0.022 2.00e-02 2.50e+03 pdb=" O ASN A 82 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU A 83 " -0.007 2.00e-02 2.50e+03 ... (remaining 619 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 532 2.76 - 3.29: 3664 3.29 - 3.83: 6165 3.83 - 4.36: 7026 4.36 - 4.90: 12093 Nonbonded interactions: 29480 Sorted by model distance: nonbonded pdb=" OG SER A 58 " pdb=" NE2 GLN B 116 " model vdw 2.219 3.120 nonbonded pdb=" NE2 GLN A 116 " pdb=" OG SER B 58 " model vdw 2.219 3.120 nonbonded pdb=" OH TYR A 154 " pdb=" OE2 GLU A 191 " model vdw 2.247 3.040 nonbonded pdb=" OH TYR B 154 " pdb=" OE2 GLU B 191 " model vdw 2.247 3.040 nonbonded pdb=" OE1 GLU C 38 " pdb=" ND2 ASN C 42 " model vdw 2.258 3.120 ... (remaining 29475 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.710 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 : 0.005 0.092 3750 Z= 0.322 Angle : 0.737 16.848 5086 Z= 0.344 Chirality : 0.045 0.314 556 Planarity : 0.003 0.024 622 Dihedral : 19.168 157.496 1322 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.38), residues: 426 helix: 1.25 (0.35), residues: 198 sheet: -0.34 (0.60), residues: 82 loop : -1.49 (0.38), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 131 HIS 0.002 0.001 HIS B 150 PHE 0.012 0.001 PHE A 56 TYR 0.004 0.001 TYR A 91 ARG 0.001 0.000 ARG D 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.423 Fit side-chains REVERT: A 45 TRP cc_start: 0.8227 (m100) cc_final: 0.7956 (m100) REVERT: A 67 LYS cc_start: 0.8728 (mmmm) cc_final: 0.8474 (mmmm) REVERT: A 87 PHE cc_start: 0.8744 (t80) cc_final: 0.8543 (t80) REVERT: A 130 CYS cc_start: 0.8322 (p) cc_final: 0.7785 (p) REVERT: A 136 LYS cc_start: 0.7947 (mmtt) cc_final: 0.7438 (mmtt) REVERT: A 152 HIS cc_start: 0.7813 (t-90) cc_final: 0.7579 (t70) REVERT: A 198 LYS cc_start: 0.8764 (mmtm) cc_final: 0.8446 (mmmm) REVERT: B 41 LEU cc_start: 0.8950 (mm) cc_final: 0.8687 (mt) REVERT: B 45 TRP cc_start: 0.8227 (m100) cc_final: 0.7955 (m100) REVERT: B 67 LYS cc_start: 0.8734 (mmmm) cc_final: 0.8478 (mmmm) REVERT: B 87 PHE cc_start: 0.8753 (t80) cc_final: 0.8545 (t80) REVERT: B 130 CYS cc_start: 0.8324 (p) cc_final: 0.7783 (p) REVERT: B 136 LYS cc_start: 0.7955 (mmtt) cc_final: 0.7446 (mmtt) REVERT: B 152 HIS cc_start: 0.7806 (t-90) cc_final: 0.7576 (t70) REVERT: B 198 LYS cc_start: 0.8765 (mmtm) cc_final: 0.8446 (mmmm) REVERT: C 25 PHE cc_start: 0.4370 (m-10) cc_final: 0.3971 (m-10) REVERT: C 42 ASN cc_start: 0.8145 (m-40) cc_final: 0.7757 (m-40) REVERT: D 25 PHE cc_start: 0.4364 (m-10) cc_final: 0.3958 (m-10) REVERT: D 42 ASN cc_start: 0.8143 (m-40) cc_final: 0.7756 (m-40) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1986 time to fit residues: 32.3429 Evaluate side-chains 121 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 82 ASN A 161 ASN A 185 GLN B 57 GLN B 82 ASN B 161 ASN B 185 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3750 Z= 0.239 Angle : 0.509 4.306 5086 Z= 0.284 Chirality : 0.043 0.163 556 Planarity : 0.003 0.027 622 Dihedral : 16.976 149.782 516 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.06 % Allowed : 11.60 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.39), residues: 426 helix: 2.52 (0.33), residues: 212 sheet: -0.42 (0.57), residues: 88 loop : -1.08 (0.46), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 149 HIS 0.002 0.001 HIS B 204 PHE 0.010 0.001 PHE B 56 TYR 0.014 0.001 TYR A 74 ARG 0.003 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.445 Fit side-chains REVERT: A 67 LYS cc_start: 0.8711 (mmmm) cc_final: 0.8009 (mmmm) REVERT: A 130 CYS cc_start: 0.8549 (p) cc_final: 0.7642 (p) REVERT: A 185 GLN cc_start: 0.8698 (tm130) cc_final: 0.8307 (tm130) REVERT: A 193 ARG cc_start: 0.8685 (ptm160) cc_final: 0.8233 (ptm160) REVERT: A 198 LYS cc_start: 0.8808 (mmtm) cc_final: 0.8480 (mmmm) REVERT: B 43 PHE cc_start: 0.7725 (m-10) cc_final: 0.7416 (m-80) REVERT: B 67 LYS cc_start: 0.8718 (mmmm) cc_final: 0.8014 (mmmm) REVERT: B 130 CYS cc_start: 0.8548 (p) cc_final: 0.7637 (p) REVERT: B 193 ARG cc_start: 0.8695 (ptm160) cc_final: 0.8249 (ptm160) REVERT: B 198 LYS cc_start: 0.8810 (mmtm) cc_final: 0.8481 (mmmm) REVERT: C 42 ASN cc_start: 0.8481 (m-40) cc_final: 0.8050 (m-40) REVERT: D 42 ASN cc_start: 0.8482 (m-40) cc_final: 0.8050 (m-40) outliers start: 8 outliers final: 4 residues processed: 131 average time/residue: 0.1863 time to fit residues: 29.0504 Evaluate side-chains 119 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 34 optimal weight: 0.1980 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 0.0010 chunk 19 optimal weight: 0.4980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN B 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3750 Z= 0.167 Angle : 0.479 4.248 5086 Z= 0.266 Chirality : 0.041 0.141 556 Planarity : 0.003 0.028 622 Dihedral : 16.009 144.466 516 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.58 % Allowed : 13.92 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.40), residues: 426 helix: 2.81 (0.33), residues: 222 sheet: -0.59 (0.58), residues: 84 loop : -1.60 (0.44), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 149 HIS 0.002 0.001 HIS B 204 PHE 0.009 0.001 PHE B 207 TYR 0.008 0.001 TYR A 74 ARG 0.004 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.538 Fit side-chains REVERT: A 109 TYR cc_start: 0.8856 (m-80) cc_final: 0.8612 (m-80) REVERT: A 128 TRP cc_start: 0.8151 (t60) cc_final: 0.7563 (t60) REVERT: A 130 CYS cc_start: 0.8641 (p) cc_final: 0.7712 (p) REVERT: A 150 HIS cc_start: 0.7609 (m-70) cc_final: 0.7172 (m-70) REVERT: A 155 ASP cc_start: 0.8014 (m-30) cc_final: 0.7341 (t0) REVERT: A 185 GLN cc_start: 0.8701 (tm130) cc_final: 0.8363 (tm130) REVERT: A 193 ARG cc_start: 0.8736 (ptm160) cc_final: 0.8332 (ptm160) REVERT: A 198 LYS cc_start: 0.8825 (mmtm) cc_final: 0.8462 (mmmm) REVERT: B 109 TYR cc_start: 0.8856 (m-80) cc_final: 0.8599 (m-80) REVERT: B 128 TRP cc_start: 0.8150 (t60) cc_final: 0.7563 (t60) REVERT: B 130 CYS cc_start: 0.8638 (p) cc_final: 0.7708 (p) REVERT: B 150 HIS cc_start: 0.7584 (m-70) cc_final: 0.7137 (m-70) REVERT: B 155 ASP cc_start: 0.8007 (m-30) cc_final: 0.7339 (t0) REVERT: B 185 GLN cc_start: 0.8700 (tm130) cc_final: 0.8359 (tm130) REVERT: B 193 ARG cc_start: 0.8735 (ptm160) cc_final: 0.8332 (ptm160) REVERT: B 198 LYS cc_start: 0.8828 (mmtm) cc_final: 0.8468 (mmmm) REVERT: C 29 ARG cc_start: 0.7146 (ttt-90) cc_final: 0.6641 (mtt-85) REVERT: C 42 ASN cc_start: 0.8452 (m-40) cc_final: 0.8028 (m-40) REVERT: D 29 ARG cc_start: 0.7142 (ttt-90) cc_final: 0.6622 (mtt-85) REVERT: D 42 ASN cc_start: 0.8452 (m-40) cc_final: 0.8027 (m-40) outliers start: 10 outliers final: 8 residues processed: 124 average time/residue: 0.1899 time to fit residues: 27.9554 Evaluate side-chains 122 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 129 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN B 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3750 Z= 0.282 Angle : 0.507 4.384 5086 Z= 0.280 Chirality : 0.042 0.146 556 Planarity : 0.003 0.027 622 Dihedral : 15.968 144.133 516 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.64 % Allowed : 13.40 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.41), residues: 426 helix: 2.97 (0.34), residues: 224 sheet: -0.89 (0.54), residues: 90 loop : -1.25 (0.47), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 149 HIS 0.003 0.001 HIS B 204 PHE 0.011 0.001 PHE A 56 TYR 0.009 0.001 TYR B 109 ARG 0.003 0.001 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 130 CYS cc_start: 0.8634 (p) cc_final: 0.7750 (p) REVERT: A 193 ARG cc_start: 0.8783 (ptm160) cc_final: 0.8403 (ptm160) REVERT: A 198 LYS cc_start: 0.8825 (mmtm) cc_final: 0.8469 (mmmm) REVERT: B 130 CYS cc_start: 0.8629 (p) cc_final: 0.7743 (p) REVERT: B 193 ARG cc_start: 0.8783 (ptm160) cc_final: 0.8404 (ptm160) REVERT: B 198 LYS cc_start: 0.8825 (mmtm) cc_final: 0.8469 (mmmm) REVERT: C 42 ASN cc_start: 0.8449 (m-40) cc_final: 0.8005 (m-40) REVERT: D 42 ASN cc_start: 0.8449 (m-40) cc_final: 0.8005 (m-40) outliers start: 18 outliers final: 12 residues processed: 117 average time/residue: 0.1759 time to fit residues: 24.5487 Evaluate side-chains 116 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 82 ASN B 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3750 Z= 0.212 Angle : 0.479 4.389 5086 Z= 0.268 Chirality : 0.041 0.136 556 Planarity : 0.003 0.027 622 Dihedral : 15.742 140.035 516 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.09 % Allowed : 13.66 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.40), residues: 426 helix: 2.92 (0.33), residues: 224 sheet: -0.63 (0.53), residues: 88 loop : -1.41 (0.47), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 149 HIS 0.002 0.001 HIS A 204 PHE 0.014 0.001 PHE A 207 TYR 0.011 0.001 TYR B 74 ARG 0.004 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 CYS cc_start: 0.8637 (p) cc_final: 0.7767 (p) REVERT: A 150 HIS cc_start: 0.7388 (m-70) cc_final: 0.6904 (m-70) REVERT: A 155 ASP cc_start: 0.8217 (m-30) cc_final: 0.7083 (t0) REVERT: A 193 ARG cc_start: 0.8797 (ptm160) cc_final: 0.8367 (ptm160) REVERT: A 198 LYS cc_start: 0.8846 (mmtm) cc_final: 0.8482 (mmmm) REVERT: B 43 PHE cc_start: 0.7772 (m-10) cc_final: 0.7569 (m-10) REVERT: B 130 CYS cc_start: 0.8634 (p) cc_final: 0.7761 (p) REVERT: B 150 HIS cc_start: 0.7387 (m-70) cc_final: 0.6896 (m-70) REVERT: B 155 ASP cc_start: 0.8210 (m-30) cc_final: 0.7084 (t0) REVERT: B 193 ARG cc_start: 0.8795 (ptm160) cc_final: 0.8366 (ptm160) REVERT: B 198 LYS cc_start: 0.8848 (mmtm) cc_final: 0.8483 (mmmm) REVERT: C 42 ASN cc_start: 0.8453 (m-40) cc_final: 0.8021 (m-40) REVERT: D 42 ASN cc_start: 0.8453 (m-40) cc_final: 0.8019 (m-40) outliers start: 12 outliers final: 8 residues processed: 117 average time/residue: 0.1807 time to fit residues: 25.4218 Evaluate side-chains 111 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 82 ASN B 78 GLN B 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3750 Z= 0.233 Angle : 0.503 4.675 5086 Z= 0.275 Chirality : 0.041 0.141 556 Planarity : 0.003 0.027 622 Dihedral : 15.531 138.507 516 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.12 % Allowed : 12.89 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.40), residues: 426 helix: 2.93 (0.33), residues: 224 sheet: -0.65 (0.53), residues: 88 loop : -1.37 (0.47), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 149 HIS 0.002 0.000 HIS B 204 PHE 0.015 0.001 PHE B 207 TYR 0.010 0.001 TYR B 145 ARG 0.004 0.000 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 CYS cc_start: 0.8613 (p) cc_final: 0.7746 (p) REVERT: A 155 ASP cc_start: 0.8268 (m-30) cc_final: 0.7984 (t0) REVERT: A 193 ARG cc_start: 0.8794 (ptm160) cc_final: 0.8347 (ptm160) REVERT: A 198 LYS cc_start: 0.8850 (mmtm) cc_final: 0.8515 (mmmm) REVERT: B 130 CYS cc_start: 0.8611 (p) cc_final: 0.7744 (p) REVERT: B 155 ASP cc_start: 0.8263 (m-30) cc_final: 0.7977 (t0) REVERT: B 165 ASP cc_start: 0.8516 (m-30) cc_final: 0.8287 (m-30) REVERT: B 193 ARG cc_start: 0.8793 (ptm160) cc_final: 0.8345 (ptm160) REVERT: B 198 LYS cc_start: 0.8850 (mmtm) cc_final: 0.8509 (mmmm) REVERT: C 42 ASN cc_start: 0.8393 (m-40) cc_final: 0.7962 (m-40) REVERT: D 42 ASN cc_start: 0.8392 (m-40) cc_final: 0.7959 (m-40) outliers start: 16 outliers final: 10 residues processed: 122 average time/residue: 0.1775 time to fit residues: 25.9597 Evaluate side-chains 122 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 40 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN B 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3750 Z= 0.199 Angle : 0.488 4.554 5086 Z= 0.269 Chirality : 0.041 0.143 556 Planarity : 0.003 0.027 622 Dihedral : 15.270 136.885 516 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.61 % Allowed : 13.66 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.40), residues: 426 helix: 2.97 (0.33), residues: 224 sheet: -0.57 (0.54), residues: 88 loop : -1.30 (0.47), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 149 HIS 0.002 0.000 HIS B 204 PHE 0.015 0.001 PHE B 207 TYR 0.009 0.001 TYR B 74 ARG 0.003 0.000 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 CYS cc_start: 0.8626 (p) cc_final: 0.7758 (p) REVERT: A 193 ARG cc_start: 0.8815 (ptm160) cc_final: 0.8346 (ptm160) REVERT: A 198 LYS cc_start: 0.8825 (mmtm) cc_final: 0.8446 (mmmm) REVERT: B 130 CYS cc_start: 0.8624 (p) cc_final: 0.7756 (p) REVERT: B 193 ARG cc_start: 0.8785 (ptm160) cc_final: 0.8319 (ptm160) REVERT: B 198 LYS cc_start: 0.8838 (mmtm) cc_final: 0.8462 (mmmm) REVERT: C 42 ASN cc_start: 0.8405 (m-40) cc_final: 0.7979 (m-40) REVERT: D 42 ASN cc_start: 0.8403 (m-40) cc_final: 0.7976 (m-40) outliers start: 14 outliers final: 10 residues processed: 122 average time/residue: 0.1922 time to fit residues: 27.9603 Evaluate side-chains 119 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 26 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 36 optimal weight: 0.0170 chunk 38 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3750 Z= 0.179 Angle : 0.505 5.706 5086 Z= 0.274 Chirality : 0.041 0.144 556 Planarity : 0.003 0.027 622 Dihedral : 14.791 135.754 516 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.06 % Allowed : 15.21 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.40), residues: 426 helix: 2.98 (0.33), residues: 224 sheet: -0.54 (0.54), residues: 88 loop : -1.25 (0.47), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 149 HIS 0.002 0.000 HIS B 204 PHE 0.025 0.002 PHE A 207 TYR 0.015 0.001 TYR B 74 ARG 0.004 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8857 (mmm) cc_final: 0.8360 (mmt) REVERT: A 130 CYS cc_start: 0.8630 (p) cc_final: 0.7776 (p) REVERT: A 150 HIS cc_start: 0.7232 (m-70) cc_final: 0.6812 (m-70) REVERT: A 155 ASP cc_start: 0.8248 (m-30) cc_final: 0.7056 (t0) REVERT: A 193 ARG cc_start: 0.8827 (ptm160) cc_final: 0.8335 (ptm-80) REVERT: A 198 LYS cc_start: 0.8809 (mmtm) cc_final: 0.8464 (mmmm) REVERT: B 125 MET cc_start: 0.8856 (mmm) cc_final: 0.8357 (mmt) REVERT: B 130 CYS cc_start: 0.8625 (p) cc_final: 0.7772 (p) REVERT: B 150 HIS cc_start: 0.7229 (m-70) cc_final: 0.6810 (m-70) REVERT: B 155 ASP cc_start: 0.8245 (m-30) cc_final: 0.7054 (t0) REVERT: B 193 ARG cc_start: 0.8824 (ptm160) cc_final: 0.8335 (ptm-80) REVERT: B 198 LYS cc_start: 0.8804 (mmtm) cc_final: 0.8461 (mmmm) REVERT: C 42 ASN cc_start: 0.8423 (m-40) cc_final: 0.7997 (m-40) REVERT: D 42 ASN cc_start: 0.8423 (m-40) cc_final: 0.7997 (m-40) outliers start: 8 outliers final: 7 residues processed: 121 average time/residue: 0.1709 time to fit residues: 24.9309 Evaluate side-chains 122 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain C residue 26 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3750 Z= 0.238 Angle : 0.530 5.805 5086 Z= 0.287 Chirality : 0.041 0.146 556 Planarity : 0.003 0.027 622 Dihedral : 14.606 134.726 516 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.84 % Allowed : 16.24 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.40), residues: 426 helix: 3.16 (0.33), residues: 226 sheet: -0.41 (0.54), residues: 88 loop : -1.26 (0.48), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 149 HIS 0.002 0.000 HIS B 204 PHE 0.025 0.002 PHE B 207 TYR 0.009 0.001 TYR B 74 ARG 0.004 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 CYS cc_start: 0.8612 (p) cc_final: 0.7756 (p) REVERT: A 150 HIS cc_start: 0.7284 (m-70) cc_final: 0.6749 (m-70) REVERT: A 155 ASP cc_start: 0.8283 (m-30) cc_final: 0.7023 (t0) REVERT: A 193 ARG cc_start: 0.8783 (ptm160) cc_final: 0.8318 (ptm160) REVERT: A 198 LYS cc_start: 0.8779 (mmtm) cc_final: 0.8448 (mmmm) REVERT: A 209 GLU cc_start: 0.8494 (tt0) cc_final: 0.8102 (tp30) REVERT: B 130 CYS cc_start: 0.8609 (p) cc_final: 0.7754 (p) REVERT: B 150 HIS cc_start: 0.7270 (m-70) cc_final: 0.6735 (m-70) REVERT: B 155 ASP cc_start: 0.8295 (m-30) cc_final: 0.7039 (t0) REVERT: B 193 ARG cc_start: 0.8782 (ptm160) cc_final: 0.8319 (ptm160) REVERT: B 198 LYS cc_start: 0.8791 (mmtm) cc_final: 0.8455 (mmmm) REVERT: C 42 ASN cc_start: 0.8421 (m-40) cc_final: 0.7997 (m-40) REVERT: C 44 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7970 (tp30) REVERT: D 42 ASN cc_start: 0.8420 (m-40) cc_final: 0.7995 (m-40) REVERT: D 44 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7975 (tp30) outliers start: 11 outliers final: 10 residues processed: 119 average time/residue: 0.1840 time to fit residues: 26.2382 Evaluate side-chains 121 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 0.0470 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 0.0270 chunk 6 optimal weight: 0.7980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3750 Z= 0.190 Angle : 0.539 6.097 5086 Z= 0.287 Chirality : 0.041 0.147 556 Planarity : 0.003 0.027 622 Dihedral : 14.047 132.950 516 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.32 % Allowed : 17.27 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.40), residues: 426 helix: 3.20 (0.32), residues: 226 sheet: -0.37 (0.55), residues: 88 loop : -1.13 (0.49), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 149 HIS 0.002 0.000 HIS A 204 PHE 0.027 0.002 PHE A 207 TYR 0.011 0.001 TYR B 74 ARG 0.004 0.001 ARG A 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 CYS cc_start: 0.8656 (p) cc_final: 0.7845 (p) REVERT: A 150 HIS cc_start: 0.7295 (m-70) cc_final: 0.6800 (m-70) REVERT: A 155 ASP cc_start: 0.8265 (m-30) cc_final: 0.7049 (t0) REVERT: A 193 ARG cc_start: 0.8812 (ptm160) cc_final: 0.8339 (ptm160) REVERT: A 198 LYS cc_start: 0.8796 (mmtm) cc_final: 0.8463 (mmmm) REVERT: A 209 GLU cc_start: 0.8512 (tt0) cc_final: 0.8109 (tp30) REVERT: B 130 CYS cc_start: 0.8655 (p) cc_final: 0.7841 (p) REVERT: B 150 HIS cc_start: 0.7265 (m-70) cc_final: 0.6764 (m-70) REVERT: B 155 ASP cc_start: 0.8272 (m-30) cc_final: 0.7062 (t0) REVERT: B 193 ARG cc_start: 0.8793 (ptm160) cc_final: 0.8322 (ptm160) REVERT: B 198 LYS cc_start: 0.8778 (mmtm) cc_final: 0.8450 (mmmm) REVERT: B 209 GLU cc_start: 0.8490 (tt0) cc_final: 0.8101 (tp30) REVERT: C 42 ASN cc_start: 0.8411 (m-40) cc_final: 0.7976 (m-40) REVERT: C 44 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7975 (tp30) REVERT: D 42 ASN cc_start: 0.8410 (m-40) cc_final: 0.7976 (m-40) REVERT: D 44 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7979 (tp30) outliers start: 9 outliers final: 7 residues processed: 122 average time/residue: 0.1830 time to fit residues: 26.5511 Evaluate side-chains 126 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain D residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.0970 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.0670 chunk 41 optimal weight: 0.8980 overall best weight: 0.4116 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.117548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.088271 restraints weight = 5871.400| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 3.13 r_work: 0.2947 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3750 Z= 0.180 Angle : 0.523 6.046 5086 Z= 0.280 Chirality : 0.041 0.150 556 Planarity : 0.003 0.027 622 Dihedral : 12.914 128.990 516 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.06 % Allowed : 18.30 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.40), residues: 426 helix: 3.24 (0.32), residues: 226 sheet: -0.32 (0.55), residues: 88 loop : -1.10 (0.49), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 149 HIS 0.002 0.000 HIS A 204 PHE 0.027 0.002 PHE B 207 TYR 0.010 0.001 TYR A 74 ARG 0.004 0.001 ARG B 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1389.05 seconds wall clock time: 25 minutes 57.50 seconds (1557.50 seconds total)