Starting phenix.real_space_refine on Fri May 9 13:43:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pij_17683/05_2025/8pij_17683.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pij_17683/05_2025/8pij_17683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pij_17683/05_2025/8pij_17683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pij_17683/05_2025/8pij_17683.map" model { file = "/net/cci-nas-00/data/ceres_data/8pij_17683/05_2025/8pij_17683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pij_17683/05_2025/8pij_17683.cif" } resolution = 2.9 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= 0.022 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 1 5.49 5 S 10 5.16 5 C 1362 2.51 5 N 376 2.21 5 O 442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2191 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1197 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 965 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'G3P': 1, 'WKE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.58, per 1000 atoms: 1.18 Number of scatterers: 2191 At special positions: 0 Unit cell: (71.61, 65.1, 117.18, 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 10 16.00 P 1 15.00 O 442 8.00 N 376 7.00 C 1362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 154 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 98 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 111 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 288.0 milliseconds 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 530 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 4 sheets defined 24.7% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 2 through 18 removed outlier: 3.511A pdb=" N LEU A 6 " --> pdb=" O THR A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 42 removed outlier: 4.404A pdb=" N TYR A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 55 removed outlier: 3.844A pdb=" N TYR A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 146 through 150 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.906A pdb=" N THR B 93 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 83 removed outlier: 3.727A pdb=" N SER A 79 " --> pdb=" O GLN A 90 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 121 " --> pdb=" O SER A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 9 removed outlier: 3.556A pdb=" N GLN B 5 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 14 removed outlier: 3.582A pdb=" N VAL B 14 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 125 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE B 36 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 51 " --> pdb=" O TRP B 38 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ARG B 40 " --> pdb=" O GLY B 49 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLY B 49 " --> pdb=" O ARG B 40 " (cutoff:3.500A) 85 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: 0.54 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 619 1.33 - 1.45: 377 1.45 - 1.57: 1215 1.57 - 1.69: 1 1.69 - 1.81: 14 Bond restraints: 2226 Sorted by residual: bond pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " ideal model delta sigma weight residual 1.726 1.608 0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" CA MET B 116 " pdb=" C MET B 116 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.25e-02 6.40e+03 6.93e+00 bond pdb=" CA VAL B 110 " pdb=" C VAL B 110 " ideal model delta sigma weight residual 1.523 1.491 0.031 1.28e-02 6.10e+03 5.91e+00 bond pdb=" CA SER B 115 " pdb=" C SER B 115 " ideal model delta sigma weight residual 1.523 1.491 0.033 1.34e-02 5.57e+03 5.89e+00 bond pdb=" CA SER B 112 " pdb=" C SER B 112 " ideal model delta sigma weight residual 1.521 1.497 0.025 1.23e-02 6.61e+03 3.99e+00 ... (remaining 2221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 2968 1.85 - 3.70: 40 3.70 - 5.55: 8 5.55 - 7.40: 2 7.40 - 9.25: 1 Bond angle restraints: 3019 Sorted by residual: angle pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " pdb=" O4P G3P A 201 " ideal model delta sigma weight residual 100.65 109.90 -9.25 3.00e+00 1.11e-01 9.51e+00 angle pdb=" N ASP B 109 " pdb=" CA ASP B 109 " pdb=" CB ASP B 109 " ideal model delta sigma weight residual 111.65 107.89 3.76 1.40e+00 5.10e-01 7.20e+00 angle pdb=" CA TYR B 113 " pdb=" CB TYR B 113 " pdb=" CG TYR B 113 " ideal model delta sigma weight residual 113.90 118.11 -4.21 1.80e+00 3.09e-01 5.46e+00 angle pdb=" C PHE B 29 " pdb=" CA PHE B 29 " pdb=" CB PHE B 29 " ideal model delta sigma weight residual 110.42 114.66 -4.24 1.99e+00 2.53e-01 4.55e+00 angle pdb=" N SER B 114 " pdb=" CA SER B 114 " pdb=" C SER B 114 " ideal model delta sigma weight residual 109.50 112.74 -3.24 1.58e+00 4.01e-01 4.20e+00 ... (remaining 3014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.62: 1217 24.62 - 49.23: 108 49.23 - 73.84: 26 73.84 - 98.46: 0 98.46 - 123.07: 2 Dihedral angle restraints: 1353 sinusoidal: 524 harmonic: 829 Sorted by residual: dihedral pdb=" C8 WKE A 202 " pdb=" C10 WKE A 202 " pdb=" C9 WKE A 202 " pdb=" O5 WKE A 202 " ideal model delta sinusoidal sigma weight residual 173.56 -63.37 -123.07 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" O4 WKE A 202 " pdb=" C10 WKE A 202 " pdb=" C9 WKE A 202 " pdb=" O5 WKE A 202 " ideal model delta sinusoidal sigma weight residual -63.24 56.71 -119.95 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" N ARG B 47 " pdb=" CA ARG B 47 " pdb=" CB ARG B 47 " pdb=" CG ARG B 47 " ideal model delta sinusoidal sigma weight residual -60.00 -119.62 59.62 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 185 0.023 - 0.046: 77 0.046 - 0.069: 52 0.069 - 0.093: 17 0.093 - 0.116: 18 Chirality restraints: 349 Sorted by residual: chirality pdb=" CA VAL B 81 " pdb=" N VAL B 81 " pdb=" C VAL B 81 " pdb=" CB VAL B 81 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.35e-01 chirality pdb=" CA VAL A 80 " pdb=" N VAL A 80 " pdb=" C VAL A 80 " pdb=" CB VAL A 80 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.29e-01 chirality pdb=" CA VAL A 77 " pdb=" N VAL A 77 " pdb=" C VAL A 77 " pdb=" CB VAL A 77 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.15e-01 ... (remaining 346 not shown) Planarity restraints: 383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7 WKE A 202 " 0.036 2.00e-02 2.50e+03 2.93e-02 1.08e+01 pdb=" C8 WKE A 202 " -0.010 2.00e-02 2.50e+03 pdb=" C9 WKE A 202 " 0.027 2.00e-02 2.50e+03 pdb=" N1 WKE A 202 " -0.046 2.00e-02 2.50e+03 pdb=" O3 WKE A 202 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 108 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C SER B 108 " 0.052 2.00e-02 2.50e+03 pdb=" O SER B 108 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP B 109 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N WKE A 202 " -0.018 2.00e-02 2.50e+03 1.15e-02 1.66e+00 pdb=" C3 WKE A 202 " 0.014 2.00e-02 2.50e+03 pdb=" C4 WKE A 202 " -0.004 2.00e-02 2.50e+03 pdb=" C5 WKE A 202 " 0.011 2.00e-02 2.50e+03 pdb=" O1 WKE A 202 " -0.003 2.00e-02 2.50e+03 ... (remaining 380 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 365 2.76 - 3.30: 1773 3.30 - 3.83: 3372 3.83 - 4.37: 3797 4.37 - 4.90: 6913 Nonbonded interactions: 16220 Sorted by model distance: nonbonded pdb=" O ALA A 31 " pdb=" OG SER A 34 " model vdw 2.231 3.040 nonbonded pdb=" OD2 ASP A 60 " pdb=" OG SER B 108 " model vdw 2.260 3.040 nonbonded pdb=" NH2 ARG B 103 " pdb=" O1 WKE A 202 " model vdw 2.348 3.120 nonbonded pdb=" OG1 THR A 81 " pdb=" O3P G3P A 201 " model vdw 2.355 3.040 nonbonded pdb=" OG SER B 56 " pdb=" O SER B 108 " model vdw 2.356 3.040 ... (remaining 16215 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: 2.720 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.390 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:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 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 0.118 2231 Z= 0.281 Angle : 0.579 9.250 3025 Z= 0.291 Chirality : 0.041 0.116 349 Planarity : 0.004 0.031 383 Dihedral : 18.971 123.074 814 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.46 % Allowed : 30.74 % Favored : 65.80 % 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: 0.25 (0.52), residues: 284 helix: 1.24 (0.72), residues: 50 sheet: 0.22 (0.59), residues: 83 loop : -0.14 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 108 HIS 0.000 0.000 HIS A 149 PHE 0.002 0.001 PHE A 119 TYR 0.018 0.001 TYR B 113 ARG 0.001 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.22915 ( 85) hydrogen bonds : angle 7.08206 ( 222) SS BOND : bond 0.00540 ( 3) SS BOND : angle 1.04455 ( 6) covalent geometry : bond 0.00430 ( 2226) covalent geometry : angle 0.57804 ( 3019) Misc. bond : bond 0.04089 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8356 (tt0) cc_final: 0.8044 (tt0) REVERT: B 75 ASP cc_start: 0.8350 (t0) cc_final: 0.7405 (t0) outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 0.8798 time to fit residues: 56.0268 Evaluate side-chains 52 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3041 r_free = 0.3041 target = 0.059972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.039530 restraints weight = 6470.209| |-----------------------------------------------------------------------------| r_work (start): 0.2491 rms_B_bonded: 3.19 r_work: 0.2373 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2265 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 2231 Z= 0.247 Angle : 0.582 4.771 3025 Z= 0.309 Chirality : 0.044 0.138 349 Planarity : 0.004 0.025 383 Dihedral : 8.424 81.464 350 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 6.49 % Allowed : 31.60 % Favored : 61.90 % 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: 0.14 (0.52), residues: 284 helix: 0.95 (0.74), residues: 51 sheet: 0.32 (0.55), residues: 92 loop : -0.28 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.009 0.002 PHE B 102 TYR 0.009 0.001 TYR B 118 ARG 0.002 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.05343 ( 85) hydrogen bonds : angle 4.83588 ( 222) SS BOND : bond 0.00093 ( 3) SS BOND : angle 0.41481 ( 6) covalent geometry : bond 0.00579 ( 2226) covalent geometry : angle 0.58237 ( 3019) Misc. bond : bond 0.00130 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.264 Fit side-chains REVERT: A 41 GLU cc_start: 0.9159 (OUTLIER) cc_final: 0.8510 (tm-30) REVERT: A 126 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8699 (ttt180) REVERT: B 20 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7257 (mp) REVERT: B 75 ASP cc_start: 0.8378 (t0) cc_final: 0.7431 (t70) REVERT: B 84 GLN cc_start: 0.8582 (tp-100) cc_final: 0.8205 (tp40) REVERT: B 85 MET cc_start: 0.8410 (mtt) cc_final: 0.8109 (mtt) REVERT: B 93 THR cc_start: 0.9367 (p) cc_final: 0.9100 (m) outliers start: 15 outliers final: 4 residues processed: 48 average time/residue: 1.1259 time to fit residues: 55.2900 Evaluate side-chains 46 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 17 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.061604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.041306 restraints weight = 6410.756| |-----------------------------------------------------------------------------| r_work (start): 0.2547 rms_B_bonded: 3.19 r_work: 0.2431 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2322 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2231 Z= 0.109 Angle : 0.496 7.097 3025 Z= 0.258 Chirality : 0.041 0.145 349 Planarity : 0.003 0.025 383 Dihedral : 5.270 52.069 346 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 6.06 % Allowed : 30.74 % Favored : 63.20 % 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: 0.26 (0.51), residues: 284 helix: 1.25 (0.76), residues: 51 sheet: 0.29 (0.53), residues: 92 loop : -0.21 (0.57), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.005 0.001 PHE B 102 TYR 0.009 0.001 TYR B 118 ARG 0.001 0.000 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 85) hydrogen bonds : angle 4.29391 ( 222) SS BOND : bond 0.00155 ( 3) SS BOND : angle 0.40083 ( 6) covalent geometry : bond 0.00250 ( 2226) covalent geometry : angle 0.49597 ( 3019) Misc. bond : bond 0.00045 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.256 Fit side-chains REVERT: A 41 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8584 (tm-30) REVERT: B 75 ASP cc_start: 0.8383 (t0) cc_final: 0.7843 (t0) REVERT: B 84 GLN cc_start: 0.8700 (tp-100) cc_final: 0.8270 (tp40) outliers start: 14 outliers final: 5 residues processed: 48 average time/residue: 1.0527 time to fit residues: 51.8200 Evaluate side-chains 43 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.4980 chunk 6 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 1 optimal weight: 0.5980 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3080 r_free = 0.3080 target = 0.061289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.040922 restraints weight = 6457.414| |-----------------------------------------------------------------------------| r_work (start): 0.2539 rms_B_bonded: 3.21 r_work: 0.2422 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2313 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2231 Z= 0.103 Angle : 0.484 5.726 3025 Z= 0.256 Chirality : 0.041 0.141 349 Planarity : 0.003 0.025 383 Dihedral : 5.074 51.488 346 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 5.19 % Allowed : 29.44 % Favored : 65.37 % 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: 0.29 (0.50), residues: 284 helix: 1.47 (0.75), residues: 51 sheet: 0.50 (0.54), residues: 77 loop : -0.35 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.005 0.001 PHE B 102 TYR 0.007 0.001 TYR B 82 ARG 0.001 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.03350 ( 85) hydrogen bonds : angle 4.07674 ( 222) SS BOND : bond 0.00127 ( 3) SS BOND : angle 0.36014 ( 6) covalent geometry : bond 0.00237 ( 2226) covalent geometry : angle 0.48412 ( 3019) Misc. bond : bond 0.00040 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.270 Fit side-chains REVERT: A 41 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: B 40 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8895 (ttp-170) REVERT: B 75 ASP cc_start: 0.8366 (t0) cc_final: 0.7815 (t0) REVERT: B 84 GLN cc_start: 0.8780 (tp-100) cc_final: 0.8419 (tp40) REVERT: B 85 MET cc_start: 0.8177 (mtt) cc_final: 0.7909 (mtt) REVERT: B 89 LYS cc_start: 0.8479 (ttmm) cc_final: 0.8226 (mtpp) REVERT: B 103 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7503 (mmp80) REVERT: B 121 LYS cc_start: 0.8772 (mppt) cc_final: 0.8557 (mppt) outliers start: 12 outliers final: 5 residues processed: 46 average time/residue: 1.1273 time to fit residues: 53.0582 Evaluate side-chains 46 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3053 r_free = 0.3053 target = 0.060200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.039624 restraints weight = 6506.191| |-----------------------------------------------------------------------------| r_work (start): 0.2499 rms_B_bonded: 3.19 r_work: 0.2383 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2276 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2231 Z= 0.155 Angle : 0.536 7.064 3025 Z= 0.278 Chirality : 0.043 0.139 349 Planarity : 0.003 0.026 383 Dihedral : 5.181 50.959 346 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 5.63 % Allowed : 29.87 % Favored : 64.50 % 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: 0.33 (0.50), residues: 284 helix: 1.51 (0.74), residues: 51 sheet: 0.61 (0.55), residues: 77 loop : -0.39 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.005 0.001 PHE B 102 TYR 0.007 0.001 TYR B 96 ARG 0.002 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.04080 ( 85) hydrogen bonds : angle 4.15137 ( 222) SS BOND : bond 0.00105 ( 3) SS BOND : angle 0.34072 ( 6) covalent geometry : bond 0.00366 ( 2226) covalent geometry : angle 0.53679 ( 3019) Misc. bond : bond 0.00070 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.262 Fit side-chains REVERT: A 41 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8628 (tm-30) REVERT: B 40 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8920 (ttp-170) REVERT: B 75 ASP cc_start: 0.8443 (t0) cc_final: 0.7894 (t0) REVERT: B 84 GLN cc_start: 0.8863 (tp-100) cc_final: 0.8534 (tp40) REVERT: B 85 MET cc_start: 0.8271 (mtt) cc_final: 0.7996 (mtt) REVERT: B 103 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7477 (mmp80) REVERT: B 121 LYS cc_start: 0.8787 (mppt) cc_final: 0.8574 (mppt) outliers start: 13 outliers final: 6 residues processed: 47 average time/residue: 1.2068 time to fit residues: 57.9644 Evaluate side-chains 45 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 1 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3027 r_free = 0.3027 target = 0.059108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.038439 restraints weight = 6505.438| |-----------------------------------------------------------------------------| r_work (start): 0.2462 rms_B_bonded: 3.18 r_work: 0.2349 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2240 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 2231 Z= 0.232 Angle : 0.575 6.086 3025 Z= 0.304 Chirality : 0.044 0.136 349 Planarity : 0.003 0.026 383 Dihedral : 5.530 50.589 346 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 6.06 % Allowed : 29.00 % Favored : 64.94 % 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: 0.21 (0.50), residues: 284 helix: 1.38 (0.74), residues: 51 sheet: 0.62 (0.56), residues: 77 loop : -0.51 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.006 0.001 PHE B 102 TYR 0.008 0.001 TYR B 118 ARG 0.004 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.04911 ( 85) hydrogen bonds : angle 4.32380 ( 222) SS BOND : bond 0.00070 ( 3) SS BOND : angle 0.37857 ( 6) covalent geometry : bond 0.00551 ( 2226) covalent geometry : angle 0.57493 ( 3019) Misc. bond : bond 0.00098 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.242 Fit side-chains REVERT: A 41 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8600 (tm-30) REVERT: A 99 GLU cc_start: 0.9392 (OUTLIER) cc_final: 0.9090 (mm-30) REVERT: B 40 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8797 (ttp-170) REVERT: B 75 ASP cc_start: 0.8423 (t0) cc_final: 0.7838 (t70) REVERT: B 85 MET cc_start: 0.8357 (mtt) cc_final: 0.8073 (mtt) REVERT: B 103 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7400 (mmp80) REVERT: B 121 LYS cc_start: 0.8787 (mppt) cc_final: 0.8571 (mppt) outliers start: 14 outliers final: 6 residues processed: 49 average time/residue: 1.2081 time to fit residues: 60.4325 Evaluate side-chains 47 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 14 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 20 optimal weight: 0.0070 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- 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 = 0.3077 r_free = 0.3077 target = 0.061262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.040768 restraints weight = 6445.944| |-----------------------------------------------------------------------------| r_work (start): 0.2535 rms_B_bonded: 3.19 r_work: 0.2422 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2312 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 2231 Z= 0.099 Angle : 0.522 7.371 3025 Z= 0.268 Chirality : 0.042 0.145 349 Planarity : 0.003 0.029 383 Dihedral : 5.069 50.946 346 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.90 % Allowed : 31.60 % Favored : 64.50 % 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: 0.59 (0.51), residues: 284 helix: 1.85 (0.78), residues: 51 sheet: 0.80 (0.57), residues: 77 loop : -0.28 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.004 0.001 PHE A 119 TYR 0.007 0.001 TYR B 96 ARG 0.001 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.03071 ( 85) hydrogen bonds : angle 3.95479 ( 222) SS BOND : bond 0.00144 ( 3) SS BOND : angle 0.39295 ( 6) covalent geometry : bond 0.00229 ( 2226) covalent geometry : angle 0.52198 ( 3019) Misc. bond : bond 0.00033 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.261 Fit side-chains REVERT: A 41 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8635 (tm-30) REVERT: B 40 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8873 (ttp-170) REVERT: B 75 ASP cc_start: 0.8426 (t0) cc_final: 0.7825 (t70) REVERT: B 84 GLN cc_start: 0.8830 (tp-100) cc_final: 0.8452 (tp40) REVERT: B 121 LYS cc_start: 0.8847 (mppt) cc_final: 0.8638 (mppt) outliers start: 9 outliers final: 7 residues processed: 45 average time/residue: 1.1141 time to fit residues: 51.3960 Evaluate side-chains 45 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 0.0270 chunk 17 optimal weight: 0.0870 chunk 14 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- 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 = 0.3088 r_free = 0.3088 target = 0.061641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.041134 restraints weight = 6617.227| |-----------------------------------------------------------------------------| r_work (start): 0.2552 rms_B_bonded: 3.25 r_work: 0.2437 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2327 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 2231 Z= 0.095 Angle : 0.493 6.077 3025 Z= 0.260 Chirality : 0.041 0.138 349 Planarity : 0.003 0.030 383 Dihedral : 4.920 50.635 346 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 5.19 % Allowed : 29.44 % Favored : 65.37 % 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: 0.62 (0.51), residues: 284 helix: 1.92 (0.77), residues: 51 sheet: 0.71 (0.55), residues: 82 loop : -0.24 (0.54), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.004 0.001 PHE B 102 TYR 0.006 0.001 TYR B 82 ARG 0.001 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.02941 ( 85) hydrogen bonds : angle 3.92054 ( 222) SS BOND : bond 0.00136 ( 3) SS BOND : angle 0.40115 ( 6) covalent geometry : bond 0.00223 ( 2226) covalent geometry : angle 0.49331 ( 3019) Misc. bond : bond 0.00032 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.254 Fit side-chains REVERT: A 41 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8093 (tt0) REVERT: B 40 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8898 (ttp-170) REVERT: B 41 GLN cc_start: 0.8597 (tp-100) cc_final: 0.7965 (tp40) REVERT: B 75 ASP cc_start: 0.8398 (t0) cc_final: 0.7781 (t70) REVERT: B 84 GLN cc_start: 0.8898 (tp-100) cc_final: 0.8492 (tp40) REVERT: B 121 LYS cc_start: 0.8819 (mppt) cc_final: 0.8598 (mppt) outliers start: 12 outliers final: 7 residues processed: 45 average time/residue: 1.1157 time to fit residues: 51.4185 Evaluate side-chains 44 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3060 r_free = 0.3060 target = 0.060511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.039925 restraints weight = 6473.082| |-----------------------------------------------------------------------------| r_work (start): 0.2507 rms_B_bonded: 3.12 r_work: 0.2394 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2283 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2231 Z= 0.151 Angle : 0.581 7.926 3025 Z= 0.297 Chirality : 0.044 0.180 349 Planarity : 0.003 0.031 383 Dihedral : 5.128 50.469 346 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.90 % Allowed : 31.60 % Favored : 64.50 % 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: 0.56 (0.51), residues: 284 helix: 1.77 (0.76), residues: 51 sheet: 0.72 (0.56), residues: 77 loop : -0.24 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.006 0.001 PHE B 102 TYR 0.008 0.001 TYR B 96 ARG 0.002 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 85) hydrogen bonds : angle 4.06102 ( 222) SS BOND : bond 0.00086 ( 3) SS BOND : angle 0.36917 ( 6) covalent geometry : bond 0.00357 ( 2226) covalent geometry : angle 0.58132 ( 3019) Misc. bond : bond 0.00057 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.269 Fit side-chains REVERT: A 41 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8620 (tm-30) REVERT: B 40 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8870 (ttp-170) REVERT: B 41 GLN cc_start: 0.8546 (tp-100) cc_final: 0.7928 (tp40) REVERT: B 75 ASP cc_start: 0.8393 (t0) cc_final: 0.7806 (t70) REVERT: B 84 GLN cc_start: 0.8891 (tp-100) cc_final: 0.8446 (tp40) outliers start: 9 outliers final: 7 residues processed: 44 average time/residue: 1.0975 time to fit residues: 49.4572 Evaluate side-chains 45 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 19 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 2 optimal weight: 0.2980 chunk 5 optimal weight: 0.1980 overall best weight: 3.2986 ------------------------------------------------------------------------------- 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 = 0.3043 r_free = 0.3043 target = 0.059796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.039152 restraints weight = 6380.567| |-----------------------------------------------------------------------------| r_work (start): 0.2482 rms_B_bonded: 3.15 r_work: 0.2368 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2259 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 2231 Z= 0.192 Angle : 0.597 7.410 3025 Z= 0.311 Chirality : 0.045 0.173 349 Planarity : 0.003 0.030 383 Dihedral : 5.365 50.391 346 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.33 % Allowed : 30.74 % Favored : 64.94 % 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: 0.40 (0.50), residues: 284 helix: 1.61 (0.75), residues: 51 sheet: 0.55 (0.56), residues: 77 loop : -0.29 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.005 0.001 PHE B 102 TYR 0.007 0.001 TYR B 118 ARG 0.003 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.04433 ( 85) hydrogen bonds : angle 4.22168 ( 222) SS BOND : bond 0.00065 ( 3) SS BOND : angle 0.36890 ( 6) covalent geometry : bond 0.00459 ( 2226) covalent geometry : angle 0.59754 ( 3019) Misc. bond : bond 0.00076 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.254 Fit side-chains REVERT: A 41 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8628 (tm-30) REVERT: B 40 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.8873 (ttp-170) REVERT: B 41 GLN cc_start: 0.8523 (tp-100) cc_final: 0.7839 (tp40) REVERT: B 75 ASP cc_start: 0.8424 (t0) cc_final: 0.7795 (t70) REVERT: B 84 GLN cc_start: 0.8945 (tp-100) cc_final: 0.8607 (mm-40) outliers start: 10 outliers final: 7 residues processed: 44 average time/residue: 1.0945 time to fit residues: 49.3450 Evaluate side-chains 43 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 14 optimal weight: 4.9990 chunk 6 optimal weight: 0.0970 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 4 optimal weight: 0.6980 overall best weight: 1.7182 ------------------------------------------------------------------------------- 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 = 0.3072 r_free = 0.3072 target = 0.060993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.040350 restraints weight = 6448.014| |-----------------------------------------------------------------------------| r_work (start): 0.2522 rms_B_bonded: 3.19 r_work: 0.2408 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2299 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2231 Z= 0.126 Angle : 0.583 8.161 3025 Z= 0.295 Chirality : 0.043 0.163 349 Planarity : 0.003 0.032 383 Dihedral : 5.169 50.628 346 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.90 % Allowed : 31.60 % Favored : 64.50 % 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: 0.52 (0.51), residues: 284 helix: 1.81 (0.77), residues: 51 sheet: 0.53 (0.56), residues: 77 loop : -0.19 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.004 0.001 PHE A 119 TYR 0.007 0.001 TYR B 96 ARG 0.002 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 85) hydrogen bonds : angle 4.09187 ( 222) SS BOND : bond 0.00114 ( 3) SS BOND : angle 0.39612 ( 6) covalent geometry : bond 0.00296 ( 2226) covalent geometry : angle 0.58376 ( 3019) Misc. bond : bond 0.00043 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2466.70 seconds wall clock time: 43 minutes 31.07 seconds (2611.07 seconds total)