Starting phenix.real_space_refine on Wed Jul 23 08:45:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iyy_61004/07_2025/9iyy_61004.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iyy_61004/07_2025/9iyy_61004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iyy_61004/07_2025/9iyy_61004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iyy_61004/07_2025/9iyy_61004.map" model { file = "/net/cci-nas-00/data/ceres_data/9iyy_61004/07_2025/9iyy_61004.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iyy_61004/07_2025/9iyy_61004.cif" } resolution = 3.13 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= 0.001 sd= 0.139 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 1592 2.51 5 N 430 2.21 5 O 482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 2534 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 432 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 52} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 381 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 44} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 935 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 786 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.58, per 1000 atoms: 1.02 Number of scatterers: 2534 At special positions: 0 Unit cell: (54.417, 65.087, 80.025, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 482 8.00 N 430 7.00 C 1592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 138 " distance=2.02 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 149 " distance=2.02 Simple disulfide: pdb=" SG CYS B 147 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 138 " distance=2.03 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 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: 0.57 Conformation dependent library (CDL) restraints added in 436.2 milliseconds 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 604 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 8 sheets defined 13.2% alpha, 37.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'B' and resid 121 through 125 removed outlier: 3.539A pdb=" N MET B 125 " --> pdb=" O ARG B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 163 Processing helix chain 'A' and resid 96 through 101 Processing helix chain 'A' and resid 156 through 166 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.670A pdb=" N THR H 91 " --> pdb=" O VAL H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.936A pdb=" N GLU L 82 " --> pdb=" O CYS L 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.501A pdb=" N CYS B 137 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.547A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N GLY H 33 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS H 98 " --> pdb=" O ASP H 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.547A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.748A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP L 34 " --> pdb=" O ILE L 46 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.748A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 18 through 22 97 hydrogen bonds defined for protein. 222 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: 0.68 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 813 1.34 - 1.46: 582 1.46 - 1.58: 1161 1.58 - 1.69: 0 1.69 - 1.81: 37 Bond restraints: 2593 Sorted by residual: bond pdb=" CB CYS B 107 " pdb=" SG CYS B 107 " ideal model delta sigma weight residual 1.808 1.781 0.027 3.30e-02 9.18e+02 6.48e-01 bond pdb=" CB LEU H 48 " pdb=" CG LEU H 48 " ideal model delta sigma weight residual 1.530 1.515 0.015 2.00e-02 2.50e+03 5.88e-01 bond pdb=" CG LEU A 104 " pdb=" CD2 LEU A 104 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.86e-01 bond pdb=" CG LEU H 45 " pdb=" CD1 LEU H 45 " ideal model delta sigma weight residual 1.521 1.499 0.022 3.30e-02 9.18e+02 4.62e-01 bond pdb=" CG LEU L 97 " pdb=" CD2 LEU L 97 " ideal model delta sigma weight residual 1.521 1.499 0.022 3.30e-02 9.18e+02 4.34e-01 ... (remaining 2588 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 3465 1.77 - 3.55: 52 3.55 - 5.32: 2 5.32 - 7.09: 2 7.09 - 8.87: 1 Bond angle restraints: 3522 Sorted by residual: angle pdb=" C ASP L 49 " pdb=" N ASP L 50 " pdb=" CA ASP L 50 " ideal model delta sigma weight residual 121.54 126.96 -5.42 1.91e+00 2.74e-01 8.06e+00 angle pdb=" CA LEU A 104 " pdb=" CB LEU A 104 " pdb=" CG LEU A 104 " ideal model delta sigma weight residual 116.30 125.17 -8.87 3.50e+00 8.16e-02 6.42e+00 angle pdb=" CA LEU A 98 " pdb=" CB LEU A 98 " pdb=" CG LEU A 98 " ideal model delta sigma weight residual 116.30 123.03 -6.73 3.50e+00 8.16e-02 3.69e+00 angle pdb=" NE ARG L 60 " pdb=" CZ ARG L 60 " pdb=" NH1 ARG L 60 " ideal model delta sigma weight residual 121.50 119.89 1.61 1.00e+00 1.00e+00 2.59e+00 angle pdb=" NE ARG H 67 " pdb=" CZ ARG H 67 " pdb=" NH1 ARG H 67 " ideal model delta sigma weight residual 121.50 119.97 1.53 1.00e+00 1.00e+00 2.34e+00 ... (remaining 3517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 1420 16.90 - 33.79: 91 33.79 - 50.68: 25 50.68 - 67.58: 4 67.58 - 84.47: 2 Dihedral angle restraints: 1542 sinusoidal: 591 harmonic: 951 Sorted by residual: dihedral pdb=" CA PHE H 95 " pdb=" C PHE H 95 " pdb=" N CYS H 96 " pdb=" CA CYS H 96 " ideal model delta harmonic sigma weight residual 180.00 164.05 15.95 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CB GLU H 6 " pdb=" CG GLU H 6 " pdb=" CD GLU H 6 " pdb=" OE1 GLU H 6 " ideal model delta sinusoidal sigma weight residual 0.00 -84.47 84.47 1 3.00e+01 1.11e-03 9.64e+00 dihedral pdb=" N CYS L 87 " pdb=" CA CYS L 87 " pdb=" CB CYS L 87 " pdb=" SG CYS L 87 " ideal model delta sinusoidal sigma weight residual -60.00 -119.59 59.59 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 202 0.026 - 0.052: 115 0.052 - 0.078: 40 0.078 - 0.104: 14 0.104 - 0.130: 18 Chirality restraints: 389 Sorted by residual: chirality pdb=" CA ILE L 20 " pdb=" N ILE L 20 " pdb=" C ILE L 20 " pdb=" CB ILE L 20 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE B 110 " pdb=" N ILE B 110 " pdb=" C ILE B 110 " pdb=" CB ILE B 110 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 ... (remaining 386 not shown) Planarity restraints: 450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG L 53 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO L 54 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO L 54 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 54 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 104 " 0.020 5.00e-02 4.00e+02 2.95e-02 1.40e+00 pdb=" N PRO A 105 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 105 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 105 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 42 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO L 43 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO L 43 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO L 43 " 0.016 5.00e-02 4.00e+02 ... (remaining 447 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 692 2.80 - 3.32: 2283 3.32 - 3.85: 4195 3.85 - 4.37: 5163 4.37 - 4.90: 9146 Nonbonded interactions: 21479 Sorted by model distance: nonbonded pdb=" NH2 ARG B 122 " pdb=" O GLY L 28 " model vdw 2.275 3.120 nonbonded pdb=" O SER H 52 " pdb=" NH1 ARG H 72 " model vdw 2.312 3.120 nonbonded pdb=" NH1 ARG H 106 " pdb=" OD1 ASP L 95 " model vdw 2.326 3.120 nonbonded pdb=" N VAL L 32 " pdb=" OD1 ASP L 50 " model vdw 2.349 3.120 nonbonded pdb=" OE1 GLN H 39 " pdb=" NE2 GLN L 37 " model vdw 2.386 3.120 ... (remaining 21474 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.820 Find NCS groups from input model: 0.020 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 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 : 0.004 0.027 2602 Z= 0.176 Angle : 0.576 8.866 3540 Z= 0.303 Chirality : 0.043 0.130 389 Planarity : 0.004 0.038 450 Dihedral : 12.045 84.468 911 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 6.12 % Allowed : 7.55 % Favored : 86.33 % 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: -0.76 (0.47), residues: 326 helix: -0.52 (0.96), residues: 30 sheet: -1.22 (0.47), residues: 108 loop : 0.11 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS H 60 PHE 0.008 0.002 PHE L 99 TYR 0.006 0.001 TYR L 2 ARG 0.003 0.001 ARG L 60 Details of bonding type rmsd hydrogen bonds : bond 0.16908 ( 82) hydrogen bonds : angle 8.99881 ( 222) SS BOND : bond 0.00416 ( 9) SS BOND : angle 0.87074 ( 18) covalent geometry : bond 0.00409 ( 2593) covalent geometry : angle 0.57425 ( 3522) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 37 time to evaluate : 0.273 Fit side-chains REVERT: A 133 MET cc_start: 0.7351 (mtp) cc_final: 0.7026 (mtp) REVERT: H 110 MET cc_start: 0.8525 (mpt) cc_final: 0.7982 (mpt) REVERT: L 26 ASN cc_start: 0.7290 (t0) cc_final: 0.7066 (t0) outliers start: 17 outliers final: 9 residues processed: 52 average time/residue: 0.1687 time to fit residues: 10.2469 Evaluate side-chains 43 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 87 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.155393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.139551 restraints weight = 2350.176| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.00 r_work: 0.3516 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2602 Z= 0.183 Angle : 0.601 9.148 3540 Z= 0.309 Chirality : 0.044 0.173 389 Planarity : 0.005 0.037 450 Dihedral : 7.420 57.475 372 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.32 % Allowed : 10.07 % Favored : 85.61 % 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: -0.72 (0.46), residues: 326 helix: -0.38 (0.92), residues: 31 sheet: -1.11 (0.50), residues: 100 loop : -0.00 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 47 HIS 0.003 0.001 HIS H 60 PHE 0.009 0.002 PHE A 161 TYR 0.006 0.001 TYR H 101 ARG 0.004 0.001 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 82) hydrogen bonds : angle 6.53394 ( 222) SS BOND : bond 0.00488 ( 9) SS BOND : angle 0.98567 ( 18) covalent geometry : bond 0.00424 ( 2593) covalent geometry : angle 0.59844 ( 3522) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.247 Fit side-chains REVERT: A 133 MET cc_start: 0.7397 (mtp) cc_final: 0.7021 (mtp) REVERT: H 110 MET cc_start: 0.8575 (mpt) cc_final: 0.8109 (mpt) REVERT: L 26 ASN cc_start: 0.7400 (t0) cc_final: 0.7055 (t0) outliers start: 12 outliers final: 10 residues processed: 45 average time/residue: 0.1253 time to fit residues: 6.9338 Evaluate side-chains 44 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 87 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 25 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.152895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.138385 restraints weight = 2366.387| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.11 r_work: 0.3472 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2602 Z= 0.216 Angle : 0.608 9.271 3540 Z= 0.310 Chirality : 0.045 0.148 389 Planarity : 0.005 0.038 450 Dihedral : 7.278 54.632 370 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.04 % Allowed : 9.71 % Favored : 85.25 % 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: -0.70 (0.46), residues: 326 helix: -0.63 (0.89), residues: 32 sheet: -0.94 (0.52), residues: 100 loop : -0.03 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 47 HIS 0.003 0.001 HIS H 60 PHE 0.010 0.002 PHE A 161 TYR 0.007 0.001 TYR H 101 ARG 0.003 0.001 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.03248 ( 82) hydrogen bonds : angle 6.41501 ( 222) SS BOND : bond 0.00528 ( 9) SS BOND : angle 1.09126 ( 18) covalent geometry : bond 0.00506 ( 2593) covalent geometry : angle 0.60462 ( 3522) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.250 Fit side-chains REVERT: H 110 MET cc_start: 0.8663 (mpt) cc_final: 0.8137 (mpt) REVERT: L 26 ASN cc_start: 0.7514 (t0) cc_final: 0.7142 (t0) outliers start: 14 outliers final: 11 residues processed: 45 average time/residue: 0.1314 time to fit residues: 7.2443 Evaluate side-chains 45 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 87 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 22 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 30 optimal weight: 0.0670 chunk 27 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.154759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.138584 restraints weight = 2337.445| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.05 r_work: 0.3507 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2602 Z= 0.171 Angle : 0.580 9.294 3540 Z= 0.294 Chirality : 0.043 0.130 389 Planarity : 0.005 0.037 450 Dihedral : 7.149 55.511 370 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.04 % Allowed : 11.15 % Favored : 83.81 % 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: -0.54 (0.46), residues: 326 helix: -0.45 (0.91), residues: 32 sheet: -0.71 (0.53), residues: 92 loop : -0.06 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS H 60 PHE 0.010 0.002 PHE A 161 TYR 0.009 0.001 TYR H 101 ARG 0.003 0.000 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.02948 ( 82) hydrogen bonds : angle 6.18612 ( 222) SS BOND : bond 0.00467 ( 9) SS BOND : angle 1.00011 ( 18) covalent geometry : bond 0.00399 ( 2593) covalent geometry : angle 0.57754 ( 3522) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.278 Fit side-chains REVERT: H 110 MET cc_start: 0.8614 (mpt) cc_final: 0.8161 (mpt) REVERT: L 26 ASN cc_start: 0.7404 (t0) cc_final: 0.7018 (t0) outliers start: 14 outliers final: 13 residues processed: 43 average time/residue: 0.1411 time to fit residues: 7.4101 Evaluate side-chains 47 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 87 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 30 optimal weight: 0.0040 chunk 3 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 0.0570 chunk 1 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 overall best weight: 0.3510 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.156997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.140945 restraints weight = 2328.010| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.03 r_work: 0.3535 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2602 Z= 0.129 Angle : 0.550 9.286 3540 Z= 0.277 Chirality : 0.042 0.132 389 Planarity : 0.004 0.035 450 Dihedral : 6.989 55.052 370 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.68 % Allowed : 12.59 % 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: -0.43 (0.47), residues: 326 helix: -0.17 (0.94), residues: 32 sheet: -0.64 (0.53), residues: 99 loop : 0.02 (0.46), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS H 60 PHE 0.010 0.002 PHE A 161 TYR 0.008 0.001 TYR H 101 ARG 0.003 0.000 ARG H 106 Details of bonding type rmsd hydrogen bonds : bond 0.02675 ( 82) hydrogen bonds : angle 5.80988 ( 222) SS BOND : bond 0.00385 ( 9) SS BOND : angle 0.84861 ( 18) covalent geometry : bond 0.00297 ( 2593) covalent geometry : angle 0.54814 ( 3522) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.298 Fit side-chains REVERT: H 110 MET cc_start: 0.8550 (mpt) cc_final: 0.8128 (mpt) outliers start: 13 outliers final: 13 residues processed: 44 average time/residue: 0.1736 time to fit residues: 9.1863 Evaluate side-chains 47 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 87 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 0.2980 chunk 19 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.156768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.140755 restraints weight = 2376.668| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.01 r_work: 0.3532 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2602 Z= 0.156 Angle : 0.564 9.167 3540 Z= 0.282 Chirality : 0.042 0.131 389 Planarity : 0.004 0.035 450 Dihedral : 6.987 55.125 369 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.04 % Allowed : 12.95 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.47), residues: 326 helix: -0.23 (0.93), residues: 32 sheet: -0.48 (0.55), residues: 92 loop : -0.01 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS H 60 PHE 0.010 0.002 PHE A 161 TYR 0.008 0.001 TYR H 101 ARG 0.001 0.000 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.02760 ( 82) hydrogen bonds : angle 5.79866 ( 222) SS BOND : bond 0.00441 ( 9) SS BOND : angle 0.94170 ( 18) covalent geometry : bond 0.00364 ( 2593) covalent geometry : angle 0.56163 ( 3522) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.271 Fit side-chains REVERT: A 98 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8145 (tt) REVERT: H 110 MET cc_start: 0.8572 (mpt) cc_final: 0.8103 (mpt) outliers start: 14 outliers final: 10 residues processed: 44 average time/residue: 0.1463 time to fit residues: 7.8347 Evaluate side-chains 45 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 87 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 0.0070 chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 0.0000 overall best weight: 0.2802 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.159548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.143650 restraints weight = 2395.229| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.04 r_work: 0.3554 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2602 Z= 0.109 Angle : 0.528 9.255 3540 Z= 0.262 Chirality : 0.041 0.132 389 Planarity : 0.004 0.034 450 Dihedral : 6.761 54.835 369 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.68 % Allowed : 12.59 % 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: -0.18 (0.47), residues: 326 helix: 0.01 (0.93), residues: 32 sheet: -0.26 (0.56), residues: 92 loop : 0.04 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 165 HIS 0.002 0.001 HIS H 60 PHE 0.009 0.001 PHE A 161 TYR 0.009 0.001 TYR H 101 ARG 0.002 0.000 ARG H 72 Details of bonding type rmsd hydrogen bonds : bond 0.02518 ( 82) hydrogen bonds : angle 5.41450 ( 222) SS BOND : bond 0.00317 ( 9) SS BOND : angle 0.72449 ( 18) covalent geometry : bond 0.00249 ( 2593) covalent geometry : angle 0.52643 ( 3522) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.272 Fit side-chains REVERT: A 98 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8114 (tt) REVERT: L 2 TYR cc_start: 0.8448 (t80) cc_final: 0.8161 (t80) REVERT: L 4 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8094 (mp) outliers start: 13 outliers final: 10 residues processed: 43 average time/residue: 0.1455 time to fit residues: 7.6306 Evaluate side-chains 46 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 87 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 0.0970 chunk 0 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.140718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.120539 restraints weight = 2506.795| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.40 r_work: 0.3176 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2602 Z= 0.145 Angle : 0.558 10.429 3540 Z= 0.275 Chirality : 0.042 0.131 389 Planarity : 0.004 0.030 450 Dihedral : 6.844 54.190 369 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.96 % Allowed : 13.67 % Favored : 82.37 % 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: -0.20 (0.47), residues: 326 helix: 0.08 (0.94), residues: 32 sheet: -0.26 (0.56), residues: 92 loop : 0.00 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 165 HIS 0.002 0.001 HIS H 60 PHE 0.009 0.002 PHE A 161 TYR 0.008 0.001 TYR H 101 ARG 0.001 0.000 ARG H 28 Details of bonding type rmsd hydrogen bonds : bond 0.02692 ( 82) hydrogen bonds : angle 5.54500 ( 222) SS BOND : bond 0.00418 ( 9) SS BOND : angle 0.91212 ( 18) covalent geometry : bond 0.00339 ( 2593) covalent geometry : angle 0.55564 ( 3522) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.324 Fit side-chains REVERT: L 4 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8166 (mp) outliers start: 11 outliers final: 9 residues processed: 42 average time/residue: 0.1541 time to fit residues: 7.8989 Evaluate side-chains 45 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 87 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 0.0770 chunk 12 optimal weight: 0.0870 chunk 28 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.1980 chunk 11 optimal weight: 0.5980 chunk 10 optimal weight: 0.0040 overall best weight: 0.1328 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.147263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.127133 restraints weight = 2491.828| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.43 r_work: 0.3256 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2602 Z= 0.085 Angle : 0.520 10.460 3540 Z= 0.252 Chirality : 0.041 0.132 389 Planarity : 0.004 0.032 450 Dihedral : 6.438 59.244 367 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.24 % Allowed : 14.75 % Favored : 82.01 % 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 (0.48), residues: 326 helix: 0.24 (0.94), residues: 32 sheet: -0.15 (0.56), residues: 100 loop : 0.16 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS H 60 PHE 0.009 0.001 PHE A 161 TYR 0.008 0.001 TYR H 101 ARG 0.001 0.000 ARG H 72 Details of bonding type rmsd hydrogen bonds : bond 0.02231 ( 82) hydrogen bonds : angle 4.76790 ( 222) SS BOND : bond 0.00243 ( 9) SS BOND : angle 0.63299 ( 18) covalent geometry : bond 0.00189 ( 2593) covalent geometry : angle 0.51951 ( 3522) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.250 Fit side-chains REVERT: A 98 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7931 (tt) REVERT: H 59 TYR cc_start: 0.8619 (m-80) cc_final: 0.8285 (m-80) REVERT: L 2 TYR cc_start: 0.8172 (t80) cc_final: 0.7838 (t80) REVERT: L 4 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7954 (mp) outliers start: 9 outliers final: 7 residues processed: 43 average time/residue: 0.1356 time to fit residues: 7.1434 Evaluate side-chains 45 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 87 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 0.0030 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 0.1980 chunk 30 optimal weight: 0.0570 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 0.2908 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.144500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.124324 restraints weight = 2474.745| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.41 r_work: 0.3222 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2602 Z= 0.109 Angle : 0.534 10.560 3540 Z= 0.259 Chirality : 0.041 0.134 389 Planarity : 0.004 0.029 450 Dihedral : 6.568 59.056 367 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.24 % Allowed : 15.83 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.48), residues: 326 helix: 0.35 (0.93), residues: 32 sheet: 0.07 (0.58), residues: 91 loop : 0.09 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS H 60 PHE 0.009 0.001 PHE A 161 TYR 0.008 0.001 TYR A 100 ARG 0.002 0.000 ARG H 106 Details of bonding type rmsd hydrogen bonds : bond 0.02420 ( 82) hydrogen bonds : angle 4.96965 ( 222) SS BOND : bond 0.00329 ( 9) SS BOND : angle 0.72783 ( 18) covalent geometry : bond 0.00252 ( 2593) covalent geometry : angle 0.53263 ( 3522) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.276 Fit side-chains REVERT: A 98 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7931 (tt) REVERT: H 59 TYR cc_start: 0.8709 (m-80) cc_final: 0.8381 (m-80) REVERT: H 83 MET cc_start: 0.8811 (mtp) cc_final: 0.8577 (mtm) REVERT: L 2 TYR cc_start: 0.8248 (t80) cc_final: 0.7943 (t80) REVERT: L 4 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8076 (mp) outliers start: 9 outliers final: 7 residues processed: 42 average time/residue: 0.1438 time to fit residues: 7.3165 Evaluate side-chains 43 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 87 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 1 optimal weight: 0.0070 chunk 23 optimal weight: 0.1980 chunk 0 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 28 optimal weight: 0.0770 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 overall best weight: 0.2756 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.144809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.124469 restraints weight = 2486.745| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.44 r_work: 0.3219 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2602 Z= 0.107 Angle : 0.533 10.401 3540 Z= 0.259 Chirality : 0.041 0.133 389 Planarity : 0.004 0.029 450 Dihedral : 6.534 58.288 367 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.24 % Allowed : 15.83 % Favored : 80.94 % 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: 0.12 (0.48), residues: 326 helix: 0.69 (0.93), residues: 31 sheet: 0.09 (0.58), residues: 91 loop : 0.07 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS H 60 PHE 0.009 0.001 PHE A 161 TYR 0.008 0.001 TYR H 101 ARG 0.004 0.000 ARG H 106 Details of bonding type rmsd hydrogen bonds : bond 0.02402 ( 82) hydrogen bonds : angle 4.96814 ( 222) SS BOND : bond 0.00322 ( 9) SS BOND : angle 0.71181 ( 18) covalent geometry : bond 0.00245 ( 2593) covalent geometry : angle 0.53205 ( 3522) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1962.06 seconds wall clock time: 34 minutes 22.65 seconds (2062.65 seconds total)