Starting phenix.real_space_refine on Sun Apr 27 07:30:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w4s_21539/04_2025/6w4s_21539.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w4s_21539/04_2025/6w4s_21539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w4s_21539/04_2025/6w4s_21539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w4s_21539/04_2025/6w4s_21539.map" model { file = "/net/cci-nas-00/data/ceres_data/6w4s_21539/04_2025/6w4s_21539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w4s_21539/04_2025/6w4s_21539.cif" } resolution = 3.2 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= -0.041 sd= 0.719 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 3240 2.51 5 N 814 2.21 5 O 903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 4986 Number of models: 1 Model: "" Number of chains: 3 Chain: "F" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3216 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 412} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 926 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 113} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 844 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 3.90, per 1000 atoms: 0.78 Number of scatterers: 4986 At special positions: 0 Unit cell: (100.158, 98.4608, 92.5192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 903 8.00 N 814 7.00 C 3240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 661.2 milliseconds 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1194 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 8 sheets defined 60.0% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 25 through 55 Processing helix chain 'F' and resid 57 through 86 removed outlier: 5.183A pdb=" N ALA F 77 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE F 78 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS F 85 " --> pdb=" O ASP F 81 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN F 86 " --> pdb=" O TRP F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 116 removed outlier: 3.649A pdb=" N ILE F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 123 Processing helix chain 'F' and resid 125 through 157 removed outlier: 4.326A pdb=" N LEU F 129 " --> pdb=" O HIS F 125 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE F 142 " --> pdb=" O THR F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 162 removed outlier: 3.507A pdb=" N VAL F 161 " --> pdb=" O ASP F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 198 removed outlier: 4.236A pdb=" N LEU F 170 " --> pdb=" O ASP F 166 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE F 186 " --> pdb=" O GLN F 182 " (cutoff:3.500A) Proline residue: F 189 - end of helix Processing helix chain 'F' and resid 200 through 230 removed outlier: 3.694A pdb=" N GLY F 206 " --> pdb=" O VAL F 202 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER F 209 " --> pdb=" O CYS F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 234 removed outlier: 3.622A pdb=" N ALA F 234 " --> pdb=" O PRO F 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 231 through 234' Processing helix chain 'F' and resid 292 through 304 removed outlier: 3.694A pdb=" N ASN F 304 " --> pdb=" O VAL F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 317 removed outlier: 3.560A pdb=" N LEU F 317 " --> pdb=" O GLY F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 335 Processing helix chain 'F' and resid 338 through 367 Processing helix chain 'F' and resid 370 through 393 removed outlier: 3.903A pdb=" N LEU F 374 " --> pdb=" O VAL F 370 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU F 386 " --> pdb=" O SER F 382 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL F 391 " --> pdb=" O CYS F 387 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE F 392 " --> pdb=" O VAL F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 484 removed outlier: 4.547A pdb=" N ILE F 467 " --> pdb=" O ILE F 463 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY F 468 " --> pdb=" O ALA F 464 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN F 483 " --> pdb=" O LEU F 479 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL F 484 " --> pdb=" O LEU F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 514 Processing helix chain 'F' and resid 516 through 546 removed outlier: 4.133A pdb=" N LEU F 525 " --> pdb=" O GLY F 521 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.863A pdb=" N GLN H 66 " --> pdb=" O ASN H 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.628A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.389A pdb=" N VAL H 107 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.772A pdb=" N CYS L 23 " --> pdb=" O PHE L 75 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE L 75 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 12 through 13 removed outlier: 3.736A pdb=" N VAL L 13 " --> pdb=" O GLU L 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'L' and resid 30 through 31 Processing sheet with id=AA7, first strand: chain 'L' and resid 49 through 52 removed outlier: 6.855A pdb=" N TRP L 39 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR L 101 " --> pdb=" O HIS L 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 49 through 52 removed outlier: 6.855A pdb=" N TRP L 39 " --> pdb=" O LEU L 51 " (cutoff:3.500A) 372 hydrogen bonds defined for protein. 1068 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: 1.56 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1539 1.34 - 1.46: 1053 1.46 - 1.58: 2463 1.58 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 5101 Sorted by residual: bond pdb=" CA ASP L 86 " pdb=" C ASP L 86 " ideal model delta sigma weight residual 1.523 1.499 0.025 1.80e-02 3.09e+03 1.86e+00 bond pdb=" CG1 ILE H 37 " pdb=" CD1 ILE H 37 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.70e-01 bond pdb=" N VAL L 62 " pdb=" CA VAL L 62 " ideal model delta sigma weight residual 1.468 1.460 0.009 1.05e-02 9.07e+03 6.89e-01 bond pdb=" CB ASP F 473 " pdb=" CG ASP F 473 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.26e-01 bond pdb=" CB ASN L 95 " pdb=" CG ASN L 95 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.09e-01 ... (remaining 5096 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 6615 1.16 - 2.33: 276 2.33 - 3.49: 45 3.49 - 4.66: 12 4.66 - 5.82: 4 Bond angle restraints: 6952 Sorted by residual: angle pdb=" N ILE F 186 " pdb=" CA ILE F 186 " pdb=" C ILE F 186 " ideal model delta sigma weight residual 113.42 110.12 3.30 1.17e+00 7.31e-01 7.93e+00 angle pdb=" C GLY F 55 " pdb=" N ASN F 56 " pdb=" CA ASN F 56 " ideal model delta sigma weight residual 121.54 126.50 -4.96 1.91e+00 2.74e-01 6.75e+00 angle pdb=" C PHE F 472 " pdb=" N ASP F 473 " pdb=" CA ASP F 473 " ideal model delta sigma weight residual 120.31 116.82 3.49 1.52e+00 4.33e-01 5.28e+00 angle pdb=" N PRO L 50 " pdb=" CA PRO L 50 " pdb=" C PRO L 50 " ideal model delta sigma weight residual 110.21 113.76 -3.55 1.64e+00 3.72e-01 4.68e+00 angle pdb=" C LEU L 54 " pdb=" N ALA L 55 " pdb=" CA ALA L 55 " ideal model delta sigma weight residual 121.54 125.67 -4.13 1.91e+00 2.74e-01 4.67e+00 ... (remaining 6947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 2640 16.75 - 33.50: 250 33.50 - 50.25: 46 50.25 - 66.99: 16 66.99 - 83.74: 5 Dihedral angle restraints: 2957 sinusoidal: 1085 harmonic: 1872 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 95 " pdb=" CB CYS H 95 " ideal model delta sinusoidal sigma weight residual 93.00 136.54 -43.54 1 1.00e+01 1.00e-02 2.64e+01 dihedral pdb=" CA TYR H 50 " pdb=" C TYR H 50 " pdb=" N ILE H 51 " pdb=" CA ILE H 51 " ideal model delta harmonic sigma weight residual 180.00 162.76 17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA LEU L 54 " pdb=" C LEU L 54 " pdb=" N ALA L 55 " pdb=" CA ALA L 55 " ideal model delta harmonic sigma weight residual 180.00 163.76 16.24 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 2954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 475 0.027 - 0.053: 211 0.053 - 0.080: 89 0.080 - 0.107: 37 0.107 - 0.133: 12 Chirality restraints: 824 Sorted by residual: chirality pdb=" CA ILE L 52 " pdb=" N ILE L 52 " pdb=" C ILE L 52 " pdb=" CB ILE L 52 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ASN F 56 " pdb=" N ASN F 56 " pdb=" C ASN F 56 " pdb=" CB ASN F 56 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA ILE H 37 " pdb=" N ILE H 37 " pdb=" C ILE H 37 " pdb=" CB ILE H 37 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 821 not shown) Planarity restraints: 849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN F 516 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO F 517 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO F 517 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 517 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 47 " 0.031 5.00e-02 4.00e+02 4.62e-02 3.42e+00 pdb=" N PRO L 48 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO L 48 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 48 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 40 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO H 41 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " -0.019 5.00e-02 4.00e+02 ... (remaining 846 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 267 2.72 - 3.27: 5211 3.27 - 3.81: 7917 3.81 - 4.36: 9283 4.36 - 4.90: 16708 Nonbonded interactions: 39386 Sorted by model distance: nonbonded pdb=" OG1 THR F 122 " pdb=" O ARG L 96 " model vdw 2.176 3.040 nonbonded pdb=" NE2 GLN L 93 " pdb=" OD1 ASN L 95 " model vdw 2.210 3.120 nonbonded pdb=" OD1 ASN H 60 " pdb=" OG SER H 62 " model vdw 2.240 3.040 nonbonded pdb=" O VAL F 67 " pdb=" OG SER F 71 " model vdw 2.247 3.040 nonbonded pdb=" OE2 GLU F 119 " pdb=" OH TYR H 33 " model vdw 2.260 3.040 ... (remaining 39381 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: 1.540 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.140 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 0.034 5103 Z= 0.187 Angle : 0.571 5.823 6956 Z= 0.331 Chirality : 0.039 0.133 824 Planarity : 0.004 0.049 849 Dihedral : 14.378 83.741 1757 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.45 % Allowed : 11.87 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.33), residues: 640 helix: 0.50 (0.27), residues: 371 sheet: -0.84 (0.53), residues: 100 loop : -3.49 (0.37), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 470 HIS 0.004 0.001 HIS F 507 PHE 0.018 0.001 PHE F 295 TYR 0.019 0.002 TYR H 78 ARG 0.002 0.000 ARG F 40 Details of bonding type rmsd hydrogen bonds : bond 0.13087 ( 358) hydrogen bonds : angle 5.96243 ( 1068) SS BOND : bond 0.00266 ( 2) SS BOND : angle 0.47295 ( 4) covalent geometry : bond 0.00419 ( 5101) covalent geometry : angle 0.57124 ( 6952) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.585 Fit side-chains REVERT: F 42 TRP cc_start: 0.8779 (OUTLIER) cc_final: 0.8337 (t-100) REVERT: F 112 MET cc_start: 0.7755 (mmm) cc_final: 0.7532 (mmm) REVERT: F 167 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7886 (mmt-90) REVERT: F 385 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8752 (tt) REVERT: F 482 GLU cc_start: 0.7658 (tt0) cc_final: 0.7205 (tt0) REVERT: F 486 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7573 (tm-30) REVERT: F 540 ARG cc_start: 0.6969 (mtm180) cc_final: 0.6696 (ttt90) REVERT: L 24 ARG cc_start: 0.7906 (mpp-170) cc_final: 0.7693 (ptt90) outliers start: 24 outliers final: 18 residues processed: 125 average time/residue: 0.1652 time to fit residues: 26.5595 Evaluate side-chains 111 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 TRP Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 167 ARG Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain F residue 473 ASP Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 484 VAL Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain F residue 527 SER Chi-restraints excluded: chain F residue 545 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 82 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 86 ASN F 99 GLN F 141 ASN F 174 ASN F 185 ASN F 481 GLN F 496 GLN F 516 ASN H 16 GLN H 35 ASN H 76 ASN H 77 HIS L 38 HIS L 78 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.128871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.104684 restraints weight = 7750.038| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.80 r_work: 0.3198 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5103 Z= 0.142 Angle : 0.541 6.267 6956 Z= 0.297 Chirality : 0.040 0.205 824 Planarity : 0.004 0.040 849 Dihedral : 7.010 58.525 731 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.27 % Allowed : 16.88 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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 (0.35), residues: 640 helix: 1.81 (0.28), residues: 370 sheet: -0.03 (0.55), residues: 102 loop : -2.76 (0.40), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 470 HIS 0.003 0.001 HIS F 507 PHE 0.012 0.001 PHE F 295 TYR 0.017 0.002 TYR H 78 ARG 0.002 0.000 ARG F 167 Details of bonding type rmsd hydrogen bonds : bond 0.05028 ( 358) hydrogen bonds : angle 4.51440 ( 1068) SS BOND : bond 0.00115 ( 2) SS BOND : angle 0.41964 ( 4) covalent geometry : bond 0.00309 ( 5101) covalent geometry : angle 0.54094 ( 6952) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.694 Fit side-chains REVERT: F 385 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8550 (tt) REVERT: F 474 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7480 (mp) REVERT: F 540 ARG cc_start: 0.6860 (mtm180) cc_final: 0.6357 (ttm-80) REVERT: L 24 ARG cc_start: 0.8126 (mpp-170) cc_final: 0.7255 (ptt90) outliers start: 23 outliers final: 15 residues processed: 119 average time/residue: 0.1864 time to fit residues: 28.2564 Evaluate side-chains 106 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain F residue 473 ASP Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 82 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 47 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 63 optimal weight: 0.0980 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 58 optimal weight: 0.0770 chunk 45 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.134043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110851 restraints weight = 7653.032| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.75 r_work: 0.3253 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5103 Z= 0.112 Angle : 0.509 6.223 6956 Z= 0.274 Chirality : 0.038 0.136 824 Planarity : 0.004 0.040 849 Dihedral : 5.737 54.696 711 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.45 % Allowed : 17.44 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.35), residues: 640 helix: 2.38 (0.28), residues: 369 sheet: -0.11 (0.55), residues: 104 loop : -2.10 (0.42), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 42 HIS 0.003 0.001 HIS L 94 PHE 0.011 0.001 PHE F 295 TYR 0.015 0.001 TYR F 220 ARG 0.003 0.000 ARG L 96 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 358) hydrogen bonds : angle 4.24717 ( 1068) SS BOND : bond 0.00151 ( 2) SS BOND : angle 0.32713 ( 4) covalent geometry : bond 0.00224 ( 5101) covalent geometry : angle 0.50921 ( 6952) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: F 133 TYR cc_start: 0.8467 (t80) cc_final: 0.8256 (t80) REVERT: F 166 ASP cc_start: 0.8172 (t0) cc_final: 0.7937 (t0) REVERT: F 385 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8410 (tt) REVERT: F 386 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7607 (tt) REVERT: F 540 ARG cc_start: 0.6832 (mtm180) cc_final: 0.6352 (ttm-80) REVERT: L 24 ARG cc_start: 0.8064 (mpp-170) cc_final: 0.7263 (ptt90) REVERT: L 37 MET cc_start: 0.7926 (tpt) cc_final: 0.7675 (tpt) outliers start: 24 outliers final: 16 residues processed: 123 average time/residue: 0.1542 time to fit residues: 24.7733 Evaluate side-chains 107 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain F residue 473 ASP Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 94 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 56 optimal weight: 0.9980 chunk 62 optimal weight: 0.0870 chunk 46 optimal weight: 0.0060 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 86 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.135156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111780 restraints weight = 7678.207| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.78 r_work: 0.3275 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5103 Z= 0.110 Angle : 0.506 7.580 6956 Z= 0.269 Chirality : 0.038 0.173 824 Planarity : 0.004 0.041 849 Dihedral : 5.620 55.440 708 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.90 % Allowed : 20.04 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.35), residues: 640 helix: 2.43 (0.28), residues: 376 sheet: 0.05 (0.55), residues: 104 loop : -1.67 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 42 HIS 0.002 0.001 HIS L 94 PHE 0.009 0.001 PHE F 295 TYR 0.015 0.001 TYR H 78 ARG 0.002 0.000 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.04218 ( 358) hydrogen bonds : angle 4.13848 ( 1068) SS BOND : bond 0.00132 ( 2) SS BOND : angle 0.62147 ( 4) covalent geometry : bond 0.00222 ( 5101) covalent geometry : angle 0.50570 ( 6952) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.624 Fit side-chains REVERT: F 385 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8297 (tt) REVERT: F 540 ARG cc_start: 0.6849 (mtm180) cc_final: 0.6353 (ttm-80) REVERT: H 48 MET cc_start: 0.8131 (mmm) cc_final: 0.7920 (mmm) REVERT: L 24 ARG cc_start: 0.8052 (mpp-170) cc_final: 0.7263 (ptt90) REVERT: L 80 HIS cc_start: 0.6944 (t70) cc_final: 0.6651 (t70) outliers start: 21 outliers final: 16 residues processed: 117 average time/residue: 0.1955 time to fit residues: 29.4852 Evaluate side-chains 110 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain F residue 473 ASP Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 94 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.132018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.108589 restraints weight = 7720.737| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.75 r_work: 0.3224 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5103 Z= 0.153 Angle : 0.544 7.090 6956 Z= 0.290 Chirality : 0.039 0.147 824 Planarity : 0.004 0.039 849 Dihedral : 5.645 55.526 708 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.64 % Allowed : 19.29 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.35), residues: 640 helix: 2.30 (0.28), residues: 376 sheet: 0.27 (0.56), residues: 100 loop : -1.63 (0.46), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 42 HIS 0.005 0.001 HIS F 507 PHE 0.013 0.001 PHE F 295 TYR 0.018 0.002 TYR H 78 ARG 0.002 0.000 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.04720 ( 358) hydrogen bonds : angle 4.26113 ( 1068) SS BOND : bond 0.00145 ( 2) SS BOND : angle 0.56173 ( 4) covalent geometry : bond 0.00346 ( 5101) covalent geometry : angle 0.54383 ( 6952) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.512 Fit side-chains REVERT: F 540 ARG cc_start: 0.6879 (mtm180) cc_final: 0.6356 (ttm-80) REVERT: L 17 GLN cc_start: 0.7213 (tt0) cc_final: 0.6996 (tt0) REVERT: L 24 ARG cc_start: 0.8139 (mpp-170) cc_final: 0.7267 (ptt90) REVERT: L 37 MET cc_start: 0.7991 (tpt) cc_final: 0.7597 (tpt) outliers start: 25 outliers final: 19 residues processed: 115 average time/residue: 0.1568 time to fit residues: 23.5473 Evaluate side-chains 108 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 94 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 4 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 0.0870 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 86 ASN H 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.133784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.110176 restraints weight = 7803.936| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.76 r_work: 0.3265 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5103 Z= 0.144 Angle : 0.542 6.814 6956 Z= 0.290 Chirality : 0.039 0.144 824 Planarity : 0.004 0.039 849 Dihedral : 4.991 51.616 704 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.82 % Allowed : 19.67 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.35), residues: 640 helix: 2.30 (0.28), residues: 374 sheet: 0.21 (0.55), residues: 102 loop : -1.54 (0.47), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 42 HIS 0.004 0.001 HIS F 507 PHE 0.012 0.001 PHE F 295 TYR 0.017 0.002 TYR H 78 ARG 0.002 0.000 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.04709 ( 358) hydrogen bonds : angle 4.25041 ( 1068) SS BOND : bond 0.00093 ( 2) SS BOND : angle 0.51006 ( 4) covalent geometry : bond 0.00322 ( 5101) covalent geometry : angle 0.54172 ( 6952) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.833 Fit side-chains REVERT: F 385 ILE cc_start: 0.8175 (tt) cc_final: 0.7675 (pt) REVERT: F 474 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7688 (mp) REVERT: F 540 ARG cc_start: 0.6879 (mtm180) cc_final: 0.6355 (ttm-80) REVERT: L 24 ARG cc_start: 0.8227 (mpp-170) cc_final: 0.7305 (ptt90) REVERT: L 37 MET cc_start: 0.7909 (tpt) cc_final: 0.7621 (tpt) REVERT: L 80 HIS cc_start: 0.6849 (t70) cc_final: 0.6631 (t70) outliers start: 26 outliers final: 22 residues processed: 114 average time/residue: 0.2139 time to fit residues: 31.7629 Evaluate side-chains 113 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 94 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 25 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 59 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 0.0770 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.135358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.112226 restraints weight = 7577.142| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.71 r_work: 0.3296 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5103 Z= 0.117 Angle : 0.525 7.647 6956 Z= 0.279 Chirality : 0.039 0.142 824 Planarity : 0.004 0.039 849 Dihedral : 4.837 51.706 704 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.90 % Allowed : 21.52 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.35), residues: 640 helix: 2.38 (0.28), residues: 375 sheet: 0.08 (0.54), residues: 106 loop : -1.32 (0.49), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 42 HIS 0.003 0.001 HIS L 94 PHE 0.010 0.001 PHE F 295 TYR 0.019 0.001 TYR F 133 ARG 0.004 0.000 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 358) hydrogen bonds : angle 4.16654 ( 1068) SS BOND : bond 0.00101 ( 2) SS BOND : angle 0.40464 ( 4) covalent geometry : bond 0.00245 ( 5101) covalent geometry : angle 0.52549 ( 6952) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.529 Fit side-chains REVERT: F 312 MET cc_start: 0.8598 (mmm) cc_final: 0.8203 (mmm) REVERT: F 385 ILE cc_start: 0.8048 (tt) cc_final: 0.7560 (pt) REVERT: F 474 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7649 (mp) REVERT: F 540 ARG cc_start: 0.6830 (mtm180) cc_final: 0.6312 (ttm-80) REVERT: H 48 MET cc_start: 0.8079 (mmm) cc_final: 0.7864 (mmm) REVERT: L 24 ARG cc_start: 0.8050 (mpp-170) cc_final: 0.7236 (ptt90) REVERT: L 80 HIS cc_start: 0.6816 (t70) cc_final: 0.6597 (t70) outliers start: 21 outliers final: 19 residues processed: 115 average time/residue: 0.1741 time to fit residues: 26.0572 Evaluate side-chains 113 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 94 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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: 58.5631 > 50: distance: 6 - 34: 17.940 distance: 10 - 38: 6.378 distance: 20 - 52: 14.521 distance: 29 - 34: 19.953 distance: 30 - 59: 10.454 distance: 34 - 35: 13.030 distance: 35 - 36: 18.765 distance: 36 - 37: 24.415 distance: 36 - 38: 21.271 distance: 37 - 65: 19.493 distance: 38 - 39: 17.902 distance: 39 - 40: 22.837 distance: 39 - 42: 19.528 distance: 40 - 41: 27.171 distance: 40 - 52: 25.053 distance: 41 - 77: 10.981 distance: 42 - 43: 3.015 distance: 43 - 44: 8.818 distance: 43 - 45: 5.809 distance: 45 - 47: 4.083 distance: 46 - 47: 3.621 distance: 47 - 49: 5.026 distance: 48 - 50: 5.860 distance: 52 - 53: 8.679 distance: 53 - 54: 14.600 distance: 53 - 56: 9.213 distance: 54 - 55: 12.825 distance: 54 - 59: 17.605 distance: 56 - 57: 12.515 distance: 59 - 60: 10.640 distance: 60 - 61: 25.995 distance: 60 - 63: 21.417 distance: 61 - 62: 3.333 distance: 61 - 65: 5.838 distance: 63 - 64: 11.929 distance: 65 - 66: 8.533 distance: 66 - 67: 15.552 distance: 66 - 69: 20.605 distance: 67 - 68: 10.360 distance: 67 - 77: 10.502 distance: 69 - 70: 4.974 distance: 70 - 71: 15.598 distance: 70 - 72: 10.398 distance: 71 - 73: 17.813 distance: 72 - 74: 13.088 distance: 73 - 75: 13.942 distance: 74 - 75: 11.234 distance: 75 - 76: 14.723 distance: 77 - 78: 12.688 distance: 78 - 79: 11.708 distance: 78 - 81: 6.895 distance: 79 - 80: 20.958 distance: 79 - 89: 31.302 distance: 81 - 82: 8.792 distance: 82 - 83: 9.773 distance: 82 - 84: 27.723 distance: 83 - 85: 6.464 distance: 84 - 86: 15.813 distance: 85 - 87: 11.184 distance: 86 - 87: 16.001 distance: 87 - 88: 22.229 distance: 89 - 90: 19.068 distance: 90 - 91: 33.523 distance: 90 - 93: 45.813 distance: 91 - 92: 25.323 distance: 91 - 97: 27.971 distance: 93 - 94: 27.669 distance: 94 - 95: 8.833 distance: 94 - 96: 14.064 distance: 97 - 98: 35.992 distance: 98 - 99: 15.243 distance: 98 - 101: 29.673 distance: 99 - 100: 8.641 distance: 99 - 106: 34.617 distance: 101 - 102: 39.925 distance: 102 - 103: 23.378 distance: 103 - 104: 40.752 distance: 103 - 105: 32.565 distance: 106 - 107: 9.095 distance: 106 - 112: 21.705 distance: 107 - 108: 31.827 distance: 107 - 110: 26.317 distance: 108 - 109: 14.921 distance: 108 - 113: 12.673 distance: 110 - 111: 20.055 distance: 111 - 112: 18.664 distance: 113 - 114: 26.029 distance: 114 - 115: 3.963 distance: 114 - 117: 16.678 distance: 115 - 120: 29.828 distance: 116 - 139: 28.106 distance: 117 - 118: 21.552 distance: 117 - 119: 18.377 distance: 163 - 172: 3.005 distance: 168 - 180: 3.066