Starting phenix.real_space_refine on Sat May 10 02:52:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cqt_45822/05_2025/9cqt_45822.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cqt_45822/05_2025/9cqt_45822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cqt_45822/05_2025/9cqt_45822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cqt_45822/05_2025/9cqt_45822.map" model { file = "/net/cci-nas-00/data/ceres_data/9cqt_45822/05_2025/9cqt_45822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cqt_45822/05_2025/9cqt_45822.cif" } resolution = 2.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 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 Fe 4 7.16 5 S 12 5.16 5 C 2914 2.51 5 N 764 2.21 5 O 1096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4790 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1050 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "B" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1110 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 137} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1050 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "D" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1110 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 137} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Chain: "C" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 87 Classifications: {'water': 87} Link IDs: {None: 86} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" O HOH B 318 " occ=0.59 Time building chain proxies: 4.38, per 1000 atoms: 0.91 Number of scatterers: 4790 At special positions: 0 Unit cell: (77.175, 72.765, 65.415, 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) Fe 4 26.01 S 12 16.00 O 1096 8.00 N 764 7.00 C 2914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 617.6 milliseconds 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1052 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 0 sheets defined 87.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 3 through 18 Processing helix chain 'A' and resid 20 through 36 Processing helix chain 'A' and resid 37 through 43 Processing helix chain 'A' and resid 52 through 72 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 80 through 90 Processing helix chain 'A' and resid 95 through 113 removed outlier: 3.789A pdb=" N LYS A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 137 Processing helix chain 'B' and resid 4 through 17 removed outlier: 3.925A pdb=" N LYS B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 36 through 46 removed outlier: 4.180A pdb=" N GLU B 43 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N SER B 44 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY B 46 " --> pdb=" O GLU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 56 Processing helix chain 'B' and resid 57 through 77 Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 85 through 95 Processing helix chain 'B' and resid 99 through 119 removed outlier: 4.040A pdb=" N PHE B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 123 through 142 Processing helix chain 'B' and resid 143 through 146 Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 20 through 36 Processing helix chain 'C' and resid 37 through 43 removed outlier: 3.506A pdb=" N THR C 41 " --> pdb=" O THR C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 72 Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 95 through 113 removed outlier: 3.809A pdb=" N LYS C 99 " --> pdb=" O PRO C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 137 Processing helix chain 'D' and resid 4 through 17 removed outlier: 3.887A pdb=" N LYS D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 36 through 46 removed outlier: 4.121A pdb=" N GLU D 43 " --> pdb=" O ARG D 40 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N SER D 44 " --> pdb=" O PHE D 41 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY D 46 " --> pdb=" O GLU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 56 Processing helix chain 'D' and resid 57 through 77 Processing helix chain 'D' and resid 80 through 85 Processing helix chain 'D' and resid 85 through 95 removed outlier: 3.544A pdb=" N LYS D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 119 removed outlier: 3.749A pdb=" N ARG D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 123 through 142 Processing helix chain 'D' and resid 143 through 146 338 hydrogen bonds defined for protein. 957 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: 1.31 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 1560 1.38 - 1.55: 3034 1.55 - 1.72: 10 1.72 - 1.89: 18 1.89 - 2.06: 16 Bond restraints: 4638 Sorted by residual: bond pdb=" N THR C 39 " pdb=" CA THR C 39 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.82e+00 bond pdb=" N VAL A 93 " pdb=" CA VAL A 93 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.24e-02 6.50e+03 9.58e+00 bond pdb=" N LYS C 40 " pdb=" CA LYS C 40 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.90e+00 bond pdb=" N LEU A 91 " pdb=" CA LEU A 91 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.23e-02 6.61e+03 7.50e+00 bond pdb=" N THR C 41 " pdb=" CA THR C 41 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.21e-02 6.83e+03 6.80e+00 ... (remaining 4633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 6014 1.20 - 2.40: 227 2.40 - 3.60: 74 3.60 - 4.80: 31 4.80 - 6.00: 12 Bond angle restraints: 6358 Sorted by residual: angle pdb=" C PHE C 36 " pdb=" N PRO C 37 " pdb=" CA PRO C 37 " ideal model delta sigma weight residual 119.56 124.15 -4.59 1.02e+00 9.61e-01 2.02e+01 angle pdb=" C ALA A 88 " pdb=" N HIS A 89 " pdb=" CA HIS A 89 " ideal model delta sigma weight residual 122.42 116.74 5.68 1.55e+00 4.16e-01 1.34e+01 angle pdb=" CA PHE C 43 " pdb=" CB PHE C 43 " pdb=" CG PHE C 43 " ideal model delta sigma weight residual 113.80 117.40 -3.60 1.00e+00 1.00e+00 1.30e+01 angle pdb=" CA THR C 41 " pdb=" C THR C 41 " pdb=" O THR C 41 " ideal model delta sigma weight residual 120.55 116.97 3.58 1.06e+00 8.90e-01 1.14e+01 angle pdb=" CA LEU A 91 " pdb=" C LEU A 91 " pdb=" O LEU A 91 " ideal model delta sigma weight residual 120.42 116.89 3.53 1.06e+00 8.90e-01 1.11e+01 ... (remaining 6353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 2259 17.75 - 35.49: 251 35.49 - 53.24: 82 53.24 - 70.99: 25 70.99 - 88.73: 9 Dihedral angle restraints: 2626 sinusoidal: 998 harmonic: 1628 Sorted by residual: dihedral pdb=" C1A HEM A 201 " pdb=" C2A HEM A 201 " pdb=" CAA HEM A 201 " pdb=" CBA HEM A 201 " ideal model delta sinusoidal sigma weight residual 180.00 93.16 86.84 2 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" C1A HEM C 201 " pdb=" C2A HEM C 201 " pdb=" CAA HEM C 201 " pdb=" CBA HEM C 201 " ideal model delta sinusoidal sigma weight residual 180.00 94.37 85.63 2 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" C1A HEM B 201 " pdb=" C2A HEM B 201 " pdb=" CAA HEM B 201 " pdb=" CBA HEM B 201 " ideal model delta sinusoidal sigma weight residual 0.00 80.08 -80.08 2 2.00e+01 2.50e-03 1.16e+01 ... (remaining 2623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 505 0.043 - 0.086: 141 0.086 - 0.129: 34 0.129 - 0.172: 5 0.172 - 0.214: 3 Chirality restraints: 688 Sorted by residual: chirality pdb=" CA PHE C 43 " pdb=" N PHE C 43 " pdb=" C PHE C 43 " pdb=" CB PHE C 43 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB THR A 134 " pdb=" CA THR A 134 " pdb=" OG1 THR A 134 " pdb=" CG2 THR A 134 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.92e-01 chirality pdb=" CB THR C 134 " pdb=" CA THR C 134 " pdb=" OG1 THR C 134 " pdb=" CG2 THR C 134 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.48e-01 ... (remaining 685 not shown) Planarity restraints: 794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 50 " 0.044 5.00e-02 4.00e+02 6.62e-02 7.00e+00 pdb=" N PRO B 51 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 51 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 51 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 94 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO C 95 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 87 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C HIS A 87 " -0.030 2.00e-02 2.50e+03 pdb=" O HIS A 87 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA A 88 " 0.011 2.00e-02 2.50e+03 ... (remaining 791 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 136 2.65 - 3.21: 4258 3.21 - 3.78: 8510 3.78 - 4.34: 11898 4.34 - 4.90: 18118 Nonbonded interactions: 42920 Sorted by model distance: nonbonded pdb=" O VAL C 93 " pdb=" OH TYR C 140 " model vdw 2.090 3.040 nonbonded pdb=" NE2 HIS D 92 " pdb="FE HEM D 201 " model vdw 2.145 3.080 nonbonded pdb=" NE2 HIS B 92 " pdb="FE HEM B 201 " model vdw 2.146 3.080 nonbonded pdb=" OD1 ASP C 85 " pdb=" O HOH C 301 " model vdw 2.174 3.040 nonbonded pdb=" O HOH C 357 " pdb=" O HOH D 346 " model vdw 2.189 3.040 ... (remaining 42915 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.59 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: 2.230 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: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 16.620 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:13.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 : 0.014 0.588 4642 Z= 0.221 Angle : 0.684 6.005 6358 Z= 0.378 Chirality : 0.043 0.214 688 Planarity : 0.006 0.066 794 Dihedral : 18.270 88.735 1574 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.44 % Allowed : 19.82 % Favored : 79.74 % 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: 3.48 (0.37), residues: 560 helix: 2.50 (0.24), residues: 428 sheet: None (None), residues: 0 loop : 1.87 (0.67), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 14 HIS 0.004 0.001 HIS D 63 PHE 0.013 0.002 PHE C 43 TYR 0.011 0.002 TYR C 42 ARG 0.004 0.001 ARG C 92 Details of bonding type rmsd hydrogen bonds : bond 0.10178 ( 338) hydrogen bonds : angle 4.29880 ( 957) covalent geometry : bond 0.00396 ( 4638) covalent geometry : angle 0.68415 ( 6358) Misc. bond : bond 0.45647 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.508 Fit side-chains REVERT: A 16 LYS cc_start: 0.7955 (mmmm) cc_final: 0.7662 (tptm) REVERT: A 90 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7543 (tttt) REVERT: B 84 THR cc_start: 0.8113 (m) cc_final: 0.7894 (m) outliers start: 2 outliers final: 0 residues processed: 81 average time/residue: 1.5125 time to fit residues: 126.5195 Evaluate side-chains 77 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 21 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 HIS C 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.153229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.130733 restraints weight = 4201.716| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.09 r_work: 0.3314 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.0672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.774 4642 Z= 0.164 Angle : 0.723 14.101 6358 Z= 0.284 Chirality : 0.041 0.168 688 Planarity : 0.006 0.060 794 Dihedral : 10.393 86.443 624 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.64 % Allowed : 14.32 % Favored : 83.04 % 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: 3.30 (0.36), residues: 560 helix: 2.33 (0.24), residues: 432 sheet: None (None), residues: 0 loop : 1.89 (0.66), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 14 HIS 0.005 0.001 HIS D 63 PHE 0.011 0.002 PHE B 118 TYR 0.010 0.002 TYR D 35 ARG 0.003 0.001 ARG C 92 Details of bonding type rmsd hydrogen bonds : bond 0.04285 ( 338) hydrogen bonds : angle 3.96965 ( 957) covalent geometry : bond 0.00339 ( 4638) covalent geometry : angle 0.72332 ( 6358) Misc. bond : bond 0.66081 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.505 Fit side-chains REVERT: A 90 LYS cc_start: 0.8129 (mppt) cc_final: 0.7633 (tttt) REVERT: B 84 THR cc_start: 0.8065 (m) cc_final: 0.7844 (m) REVERT: C 38 THR cc_start: 0.8359 (p) cc_final: 0.8116 (t) REVERT: C 60 LYS cc_start: 0.8435 (tttm) cc_final: 0.7838 (ttmp) REVERT: C 126 ASP cc_start: 0.8077 (t70) cc_final: 0.7796 (t70) outliers start: 12 outliers final: 1 residues processed: 82 average time/residue: 1.4907 time to fit residues: 126.1265 Evaluate side-chains 79 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 127 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 28 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.155852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.133745 restraints weight = 4257.055| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.07 r_work: 0.3345 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.265 4642 Z= 0.114 Angle : 0.703 15.212 6358 Z= 0.254 Chirality : 0.038 0.167 688 Planarity : 0.006 0.058 794 Dihedral : 9.983 84.860 620 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Rotamer: Outliers : 1.98 % Allowed : 15.86 % Favored : 82.16 % 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: 3.74 (0.36), residues: 560 helix: 2.65 (0.24), residues: 430 sheet: None (None), residues: 0 loop : 2.05 (0.65), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 14 HIS 0.003 0.001 HIS D 63 PHE 0.007 0.001 PHE B 118 TYR 0.007 0.001 TYR B 130 ARG 0.002 0.000 ARG C 92 Details of bonding type rmsd hydrogen bonds : bond 0.03374 ( 338) hydrogen bonds : angle 3.77657 ( 957) covalent geometry : bond 0.00265 ( 4638) covalent geometry : angle 0.70350 ( 6358) Misc. bond : bond 0.22786 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.567 Fit side-chains REVERT: A 60 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7875 (ttmp) REVERT: A 90 LYS cc_start: 0.8124 (mppt) cc_final: 0.7633 (tttt) REVERT: B 120 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7716 (ttmm) REVERT: C 38 THR cc_start: 0.8337 (p) cc_final: 0.8111 (t) REVERT: C 60 LYS cc_start: 0.8414 (tttm) cc_final: 0.7834 (ttmp) REVERT: C 126 ASP cc_start: 0.8034 (t70) cc_final: 0.7750 (t70) REVERT: D 99 ASP cc_start: 0.8060 (t70) cc_final: 0.7846 (t70) outliers start: 9 outliers final: 0 residues processed: 81 average time/residue: 1.5883 time to fit residues: 132.6642 Evaluate side-chains 71 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain B residue 120 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 3.9990 chunk 1 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.154175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.131832 restraints weight = 4289.971| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.08 r_work: 0.3327 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 4642 Z= 0.123 Angle : 0.743 16.241 6358 Z= 0.263 Chirality : 0.039 0.175 688 Planarity : 0.006 0.057 794 Dihedral : 10.036 85.971 620 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.98 % Allowed : 15.86 % Favored : 82.16 % 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: 3.68 (0.36), residues: 560 helix: 2.61 (0.24), residues: 430 sheet: None (None), residues: 0 loop : 2.02 (0.65), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 14 HIS 0.004 0.001 HIS B 116 PHE 0.009 0.001 PHE B 118 TYR 0.008 0.001 TYR D 35 ARG 0.002 0.000 ARG C 92 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 338) hydrogen bonds : angle 3.79600 ( 957) covalent geometry : bond 0.00285 ( 4638) covalent geometry : angle 0.74345 ( 6358) Misc. bond : bond 0.10312 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.563 Fit side-chains REVERT: A 60 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7882 (ttmp) REVERT: A 85 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7741 (t70) REVERT: A 90 LYS cc_start: 0.8123 (mppt) cc_final: 0.7641 (tttt) REVERT: C 60 LYS cc_start: 0.8426 (tttm) cc_final: 0.7838 (ttmp) REVERT: C 126 ASP cc_start: 0.8078 (t70) cc_final: 0.7806 (t70) outliers start: 9 outliers final: 0 residues processed: 79 average time/residue: 1.6152 time to fit residues: 131.5543 Evaluate side-chains 69 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 85 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 20 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 78 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.155114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.130911 restraints weight = 4344.487| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.20 r_work: 0.3322 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 4642 Z= 0.132 Angle : 0.765 16.863 6358 Z= 0.271 Chirality : 0.040 0.182 688 Planarity : 0.006 0.056 794 Dihedral : 10.107 85.790 620 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.42 % Allowed : 16.08 % Favored : 81.50 % 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: 3.55 (0.36), residues: 560 helix: 2.52 (0.24), residues: 430 sheet: None (None), residues: 0 loop : 1.98 (0.64), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 14 HIS 0.004 0.001 HIS B 116 PHE 0.010 0.002 PHE B 118 TYR 0.008 0.001 TYR D 35 ARG 0.002 0.000 ARG C 92 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 338) hydrogen bonds : angle 3.84560 ( 957) covalent geometry : bond 0.00305 ( 4638) covalent geometry : angle 0.76455 ( 6358) Misc. bond : bond 0.08503 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.559 Fit side-chains REVERT: A 60 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7793 (ttmp) REVERT: A 85 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7722 (t70) REVERT: A 90 LYS cc_start: 0.8132 (mppt) cc_final: 0.7576 (tttt) REVERT: C 60 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7779 (ttmp) REVERT: C 126 ASP cc_start: 0.8005 (t70) cc_final: 0.7672 (t70) REVERT: D 95 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7222 (tmtt) outliers start: 11 outliers final: 1 residues processed: 81 average time/residue: 1.6046 time to fit residues: 133.8992 Evaluate side-chains 74 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain D residue 95 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.155815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.131780 restraints weight = 4259.768| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.18 r_work: 0.3340 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 4642 Z= 0.123 Angle : 0.756 16.955 6358 Z= 0.263 Chirality : 0.039 0.181 688 Planarity : 0.006 0.056 794 Dihedral : 10.033 85.530 620 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.54 % Allowed : 17.62 % Favored : 80.84 % 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: 3.68 (0.36), residues: 560 helix: 2.62 (0.24), residues: 430 sheet: None (None), residues: 0 loop : 2.00 (0.64), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 14 HIS 0.004 0.001 HIS D 63 PHE 0.009 0.001 PHE B 118 TYR 0.008 0.001 TYR D 35 ARG 0.002 0.000 ARG D 104 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 338) hydrogen bonds : angle 3.78778 ( 957) covalent geometry : bond 0.00285 ( 4638) covalent geometry : angle 0.75617 ( 6358) Misc. bond : bond 0.08264 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.579 Fit side-chains REVERT: A 60 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7818 (ttmp) REVERT: A 85 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7699 (t70) REVERT: A 90 LYS cc_start: 0.8101 (mppt) cc_final: 0.7567 (tttt) REVERT: C 60 LYS cc_start: 0.8441 (tttm) cc_final: 0.7807 (ttmp) REVERT: C 126 ASP cc_start: 0.8012 (t70) cc_final: 0.7722 (t70) REVERT: D 95 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7223 (tmtt) outliers start: 7 outliers final: 2 residues processed: 78 average time/residue: 1.6627 time to fit residues: 133.6791 Evaluate side-chains 74 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain D residue 95 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 22 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.154764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.130922 restraints weight = 4214.459| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.17 r_work: 0.3319 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.170 4642 Z= 0.136 Angle : 0.779 17.133 6358 Z= 0.273 Chirality : 0.041 0.189 688 Planarity : 0.006 0.056 794 Dihedral : 10.131 85.970 620 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.54 % Allowed : 18.06 % Favored : 80.40 % 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: 3.59 (0.35), residues: 560 helix: 2.55 (0.24), residues: 430 sheet: None (None), residues: 0 loop : 2.00 (0.64), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 14 HIS 0.004 0.001 HIS D 63 PHE 0.010 0.002 PHE B 118 TYR 0.008 0.001 TYR D 35 ARG 0.002 0.000 ARG D 104 Details of bonding type rmsd hydrogen bonds : bond 0.04001 ( 338) hydrogen bonds : angle 3.83619 ( 957) covalent geometry : bond 0.00312 ( 4638) covalent geometry : angle 0.77924 ( 6358) Misc. bond : bond 0.11864 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.557 Fit side-chains REVERT: A 60 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7803 (ttmp) REVERT: A 85 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7744 (t70) REVERT: C 60 LYS cc_start: 0.8425 (tttm) cc_final: 0.7779 (ttmp) REVERT: C 126 ASP cc_start: 0.8021 (t70) cc_final: 0.7695 (t70) REVERT: D 95 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7220 (tmtt) outliers start: 7 outliers final: 4 residues processed: 75 average time/residue: 1.5315 time to fit residues: 118.5789 Evaluate side-chains 76 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 95 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 25 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.155564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.131597 restraints weight = 4237.372| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.18 r_work: 0.3328 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 4642 Z= 0.125 Angle : 0.770 17.229 6358 Z= 0.265 Chirality : 0.040 0.189 688 Planarity : 0.006 0.056 794 Dihedral : 10.051 85.519 620 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.54 % Allowed : 18.28 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.70 (0.36), residues: 560 helix: 2.63 (0.24), residues: 430 sheet: None (None), residues: 0 loop : 2.03 (0.64), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 14 HIS 0.004 0.001 HIS D 63 PHE 0.009 0.001 PHE B 118 TYR 0.008 0.001 TYR D 35 ARG 0.002 0.000 ARG B 104 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 338) hydrogen bonds : angle 3.78552 ( 957) covalent geometry : bond 0.00289 ( 4638) covalent geometry : angle 0.76960 ( 6358) Misc. bond : bond 0.11917 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.559 Fit side-chains REVERT: A 60 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7820 (ttmp) REVERT: A 85 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7709 (t70) REVERT: A 90 LYS cc_start: 0.8117 (mppt) cc_final: 0.7561 (tttt) REVERT: C 60 LYS cc_start: 0.8445 (tttm) cc_final: 0.7811 (ttmp) REVERT: C 126 ASP cc_start: 0.8015 (t70) cc_final: 0.7651 (t70) REVERT: D 95 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7198 (tmtt) outliers start: 7 outliers final: 2 residues processed: 78 average time/residue: 1.5744 time to fit residues: 126.6135 Evaluate side-chains 73 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain D residue 95 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 11 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.155143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.131183 restraints weight = 4269.230| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.18 r_work: 0.3325 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.153 4642 Z= 0.129 Angle : 0.780 17.244 6358 Z= 0.269 Chirality : 0.040 0.191 688 Planarity : 0.006 0.056 794 Dihedral : 10.084 85.845 620 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.32 % Allowed : 18.94 % Favored : 79.74 % 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: 3.67 (0.36), residues: 560 helix: 2.60 (0.24), residues: 430 sheet: None (None), residues: 0 loop : 2.04 (0.64), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 14 HIS 0.004 0.001 HIS D 63 PHE 0.009 0.001 PHE B 118 TYR 0.008 0.001 TYR C 140 ARG 0.003 0.000 ARG B 104 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 338) hydrogen bonds : angle 3.79656 ( 957) covalent geometry : bond 0.00295 ( 4638) covalent geometry : angle 0.77981 ( 6358) Misc. bond : bond 0.13832 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.490 Fit side-chains REVERT: A 60 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7829 (ttmp) REVERT: A 85 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7725 (t70) REVERT: C 60 LYS cc_start: 0.8420 (tttm) cc_final: 0.7768 (ttmp) REVERT: C 126 ASP cc_start: 0.8019 (t70) cc_final: 0.7678 (t70) REVERT: D 95 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7251 (tmtt) outliers start: 6 outliers final: 3 residues processed: 71 average time/residue: 1.5969 time to fit residues: 117.0608 Evaluate side-chains 73 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain D residue 95 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 32 optimal weight: 0.7980 chunk 45 optimal weight: 0.0770 chunk 27 optimal weight: 6.9990 chunk 47 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.156336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.132426 restraints weight = 4249.253| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.18 r_work: 0.3340 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 4642 Z= 0.115 Angle : 0.761 17.046 6358 Z= 0.259 Chirality : 0.039 0.187 688 Planarity : 0.006 0.057 794 Dihedral : 9.958 85.459 620 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.76 % Allowed : 18.72 % Favored : 79.52 % 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: 3.84 (0.36), residues: 560 helix: 2.72 (0.24), residues: 430 sheet: None (None), residues: 0 loop : 2.10 (0.64), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 37 HIS 0.003 0.001 HIS D 63 PHE 0.007 0.001 PHE B 118 TYR 0.007 0.001 TYR C 140 ARG 0.003 0.001 ARG D 104 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 338) hydrogen bonds : angle 3.73059 ( 957) covalent geometry : bond 0.00266 ( 4638) covalent geometry : angle 0.76113 ( 6358) Misc. bond : bond 0.11427 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.534 Fit side-chains REVERT: A 60 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7800 (ttmp) REVERT: A 85 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7687 (t70) REVERT: A 90 LYS cc_start: 0.8095 (mppt) cc_final: 0.7524 (tttt) REVERT: C 60 LYS cc_start: 0.8440 (tttm) cc_final: 0.7802 (ttmp) REVERT: C 126 ASP cc_start: 0.8003 (t70) cc_final: 0.7673 (t70) REVERT: D 95 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7228 (tmtt) outliers start: 8 outliers final: 1 residues processed: 76 average time/residue: 1.5819 time to fit residues: 124.0743 Evaluate side-chains 78 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain D residue 95 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.129 > 50: distance: 18 - 41: 3.089 distance: 22 - 49: 4.278 distance: 29 - 59: 4.965 distance: 34 - 41: 4.815 distance: 35 - 65: 7.733 distance: 41 - 42: 4.445 distance: 42 - 45: 5.431 distance: 45 - 46: 6.734 distance: 46 - 47: 3.876 distance: 46 - 48: 4.738 distance: 49 - 50: 3.344 distance: 50 - 53: 3.928 distance: 51 - 52: 7.397 distance: 51 - 59: 5.104 distance: 53 - 54: 3.081 distance: 55 - 57: 6.819 distance: 57 - 58: 6.550 distance: 59 - 60: 7.445 distance: 60 - 61: 5.212 distance: 60 - 63: 5.275 distance: 61 - 62: 11.697 distance: 61 - 65: 13.606 distance: 63 - 64: 12.298 distance: 65 - 66: 17.689 distance: 66 - 67: 3.364 distance: 66 - 69: 10.138 distance: 67 - 68: 26.185 distance: 67 - 73: 27.625 distance: 69 - 70: 14.456 distance: 70 - 71: 16.740 distance: 70 - 72: 13.883 distance: 73 - 74: 17.821 distance: 74 - 75: 5.755 distance: 74 - 77: 4.045 distance: 75 - 76: 8.076 distance: 75 - 82: 11.624 distance: 77 - 78: 12.994 distance: 78 - 79: 8.727 distance: 79 - 80: 9.329 distance: 82 - 83: 3.718 distance: 83 - 84: 6.222 distance: 83 - 86: 7.279 distance: 84 - 85: 7.768 distance: 84 - 90: 4.564 distance: 86 - 87: 4.461 distance: 87 - 88: 4.904 distance: 87 - 89: 8.278 distance: 90 - 91: 3.993 distance: 91 - 92: 4.570 distance: 91 - 94: 3.023 distance: 92 - 100: 3.937 distance: 94 - 95: 3.478 distance: 95 - 96: 4.222 distance: 95 - 97: 6.914 distance: 96 - 98: 3.681 distance: 97 - 99: 4.877 distance: 98 - 99: 4.727 distance: 101 - 102: 3.317 distance: 101 - 104: 4.057 distance: 102 - 103: 4.254 distance: 102 - 107: 3.482 distance: 104 - 105: 5.829 distance: 104 - 106: 4.588 distance: 107 - 108: 6.320 distance: 108 - 109: 5.194 distance: 108 - 111: 3.658 distance: 109 - 110: 6.100 distance: 109 - 115: 4.801 distance: 112 - 113: 5.107 distance: 115 - 116: 7.597 distance: 115 - 121: 7.890 distance: 116 - 117: 5.141 distance: 116 - 119: 10.413 distance: 117 - 118: 4.346 distance: 117 - 122: 3.115 distance: 119 - 120: 9.150 distance: 120 - 121: 16.025