Starting phenix.real_space_refine on Mon Jan 13 21:30:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dls_27514/01_2025/8dls_27514.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dls_27514/01_2025/8dls_27514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dls_27514/01_2025/8dls_27514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dls_27514/01_2025/8dls_27514.map" model { file = "/net/cci-nas-00/data/ceres_data/8dls_27514/01_2025/8dls_27514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dls_27514/01_2025/8dls_27514.cif" } resolution = 2.66 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= 0.016 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 18 5.16 5 C 2566 2.51 5 N 648 2.21 5 O 785 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4017 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2081 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 12, 'TRANS': 242} Chain breaks: 3 Chain: "H" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 976 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "L" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 3.96, per 1000 atoms: 0.99 Number of scatterers: 4017 At special positions: 0 Unit cell: (95, 61, 101, 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 18 16.00 O 785 8.00 N 648 7.00 C 2566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 113 " 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 149 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG B 1 " - " ASN A 122 " Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 436.0 milliseconds 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 920 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 10 sheets defined 2.6% alpha, 45.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.910A pdb=" N THR H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 108 removed outlier: 3.963A pdb=" N VAL L 108 " --> pdb=" O ALA L 105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 8.072A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.764A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.606A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.627A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.225A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.813A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.170A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AA6, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.164A pdb=" N GLU H 29 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR H 141 " --> pdb=" O TYR H 113 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N MET H 53 " --> pdb=" O GLY H 69 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TRP H 55 " --> pdb=" O MET H 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.164A pdb=" N GLU H 29 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR H 141 " --> pdb=" O TYR H 113 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 121 through 123 Processing sheet with id=AA9, first strand: chain 'L' and resid 24 through 27 Processing sheet with id=AB1, first strand: chain 'L' and resid 30 through 32 removed outlier: 3.758A pdb=" N ASP L 130 " --> pdb=" O SER L 31 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLN L 62 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU L 71 " --> pdb=" O GLN L 62 " (cutoff:3.500A) 144 hydrogen bonds defined for protein. 357 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: 1.04 Time building geometry restraints manager: 1.11 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: 1235 1.34 - 1.46: 1022 1.46 - 1.58: 1834 1.58 - 1.70: 0 1.70 - 1.81: 27 Bond restraints: 4118 Sorted by residual: bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.24e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.90e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.69e+00 bond pdb=" C ARG A 102 " pdb=" N GLY A 103 " ideal model delta sigma weight residual 1.327 1.307 0.020 1.11e-02 8.12e+03 3.25e+00 ... (remaining 4113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 5450 2.47 - 4.95: 130 4.95 - 7.42: 14 7.42 - 9.90: 1 9.90 - 12.37: 2 Bond angle restraints: 5597 Sorted by residual: angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 121.54 132.21 -10.67 1.91e+00 2.74e-01 3.12e+01 angle pdb=" CA LEU H 127 " pdb=" CB LEU H 127 " pdb=" CG LEU H 127 " ideal model delta sigma weight residual 116.30 128.67 -12.37 3.50e+00 8.16e-02 1.25e+01 angle pdb=" C GLN H 139 " pdb=" N GLY H 140 " pdb=" CA GLY H 140 " ideal model delta sigma weight residual 122.73 119.73 3.00 9.30e-01 1.16e+00 1.04e+01 angle pdb=" CA THR L 56 " pdb=" CB THR L 56 " pdb=" CG2 THR L 56 " ideal model delta sigma weight residual 110.50 115.81 -5.31 1.70e+00 3.46e-01 9.77e+00 angle pdb=" CA ASP A 198 " pdb=" CB ASP A 198 " pdb=" CG ASP A 198 " ideal model delta sigma weight residual 112.60 115.70 -3.10 1.00e+00 1.00e+00 9.64e+00 ... (remaining 5592 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 2319 17.40 - 34.79: 149 34.79 - 52.18: 26 52.18 - 69.57: 5 69.57 - 86.97: 5 Dihedral angle restraints: 2504 sinusoidal: 1066 harmonic: 1438 Sorted by residual: dihedral pdb=" CA ASN A 149 " pdb=" C ASN A 149 " pdb=" N LYS A 150 " pdb=" CA LYS A 150 " ideal model delta harmonic sigma weight residual 180.00 150.54 29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA LYS H 31 " pdb=" C LYS H 31 " pdb=" N LYS H 32 " pdb=" CA LYS H 32 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ILE A 128 " pdb=" C ILE A 128 " pdb=" N LYS A 129 " pdb=" CA LYS A 129 " ideal model delta harmonic sigma weight residual 180.00 -159.53 -20.47 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 2501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 572 0.097 - 0.193: 57 0.193 - 0.290: 3 0.290 - 0.386: 0 0.386 - 0.483: 3 Chirality restraints: 635 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.83e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 149 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CB THR L 56 " pdb=" CA THR L 56 " pdb=" OG1 THR L 56 " pdb=" CG2 THR L 56 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.41 2.00e-01 2.50e+01 4.19e+00 ... (remaining 632 not shown) Planarity restraints: 711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 149 " 0.005 2.00e-02 2.50e+03 2.66e-02 8.87e+00 pdb=" CG ASN A 149 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 149 " 0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN A 149 " -0.027 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 198 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.53e+00 pdb=" CG ASP A 198 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASP A 198 " -0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP A 198 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL L 83 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO L 84 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO L 84 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 84 " 0.035 5.00e-02 4.00e+02 ... (remaining 708 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1088 2.81 - 3.33: 3098 3.33 - 3.86: 6567 3.86 - 4.38: 7546 4.38 - 4.90: 13461 Nonbonded interactions: 31760 Sorted by model distance: nonbonded pdb=" OD1 ASP H 109 " pdb=" OH TYR H 113 " model vdw 2.288 3.040 nonbonded pdb=" OG SER L 90 " pdb=" OG1 THR L 97 " model vdw 2.323 3.040 nonbonded pdb=" OG1 THR H 124 " pdb=" O ASP H 126 " model vdw 2.327 3.040 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.362 3.040 nonbonded pdb=" O SER H 147 " pdb=" OG SER H 147 " model vdw 2.374 3.040 ... (remaining 31755 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: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.710 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 : 0.006 0.057 4118 Z= 0.395 Angle : 0.916 12.370 5597 Z= 0.486 Chirality : 0.063 0.483 635 Planarity : 0.007 0.069 705 Dihedral : 12.285 86.966 1572 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.37), residues: 483 helix: None (None), residues: 0 sheet: 0.15 (0.36), residues: 218 loop : -0.84 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 66 HIS 0.005 0.002 HIS L 51 PHE 0.028 0.003 PHE A 238 TYR 0.020 0.002 TYR A 160 ARG 0.014 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.422 Fit side-chains REVERT: A 15 CYS cc_start: 0.7351 (m) cc_final: 0.7117 (m) REVERT: A 153 MET cc_start: 0.8371 (mmt) cc_final: 0.8037 (mmm) REVERT: H 99 TYR cc_start: 0.7958 (m-80) cc_final: 0.7599 (m-80) REVERT: L 63 GLN cc_start: 0.8931 (tt0) cc_final: 0.8728 (tt0) REVERT: L 75 LYS cc_start: 0.8501 (mttt) cc_final: 0.8168 (mtpt) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 1.0930 time to fit residues: 111.1766 Evaluate side-chains 83 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 0.0770 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 43 optimal weight: 0.0060 overall best weight: 0.3954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN L 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.122867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.080427 restraints weight = 6285.463| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.81 r_work: 0.2963 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4118 Z= 0.194 Angle : 0.599 10.524 5597 Z= 0.306 Chirality : 0.049 0.383 635 Planarity : 0.004 0.048 705 Dihedral : 6.207 50.710 684 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.61 % Allowed : 9.89 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.39), residues: 483 helix: None (None), residues: 0 sheet: 0.31 (0.35), residues: 218 loop : -0.38 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 66 HIS 0.002 0.001 HIS A 146 PHE 0.010 0.001 PHE A 133 TYR 0.009 0.001 TYR A 269 ARG 0.003 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.494 Fit side-chains REVERT: A 129 LYS cc_start: 0.8276 (ttmm) cc_final: 0.8026 (ttmm) REVERT: A 214 ARG cc_start: 0.7714 (tpp-160) cc_final: 0.7339 (tpp-160) REVERT: H 42 LYS cc_start: 0.8925 (ttmm) cc_final: 0.8718 (tttp) REVERT: H 48 LEU cc_start: 0.8556 (tp) cc_final: 0.8205 (tt) REVERT: H 99 TYR cc_start: 0.8115 (m-80) cc_final: 0.7817 (m-80) REVERT: H 130 TYR cc_start: 0.8436 (m-80) cc_final: 0.8156 (m-80) REVERT: L 63 GLN cc_start: 0.8925 (tt0) cc_final: 0.8663 (tt0) REVERT: L 70 ARG cc_start: 0.8663 (ptt180) cc_final: 0.8442 (ppt170) REVERT: L 75 LYS cc_start: 0.8379 (mttt) cc_final: 0.8087 (mmmt) outliers start: 7 outliers final: 7 residues processed: 87 average time/residue: 1.0744 time to fit residues: 97.0325 Evaluate side-chains 87 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 39 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 0.2980 chunk 35 optimal weight: 0.0870 chunk 19 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.122496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.080163 restraints weight = 6346.594| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.83 r_work: 0.2962 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4118 Z= 0.195 Angle : 0.578 10.221 5597 Z= 0.293 Chirality : 0.047 0.345 635 Planarity : 0.004 0.042 705 Dihedral : 5.817 50.125 684 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.07 % Allowed : 12.18 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.16 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.47 (0.37), residues: 215 loop : -0.12 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 66 HIS 0.003 0.001 HIS A 49 PHE 0.017 0.001 PHE L 96 TYR 0.013 0.001 TYR H 132 ARG 0.004 0.000 ARG L 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.451 Fit side-chains REVERT: A 215 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7630 (m-30) REVERT: H 48 LEU cc_start: 0.8622 (tp) cc_final: 0.8236 (tt) REVERT: H 50 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8046 (mp0) REVERT: H 65 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7959 (pt0) REVERT: H 100 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.8073 (ttp) REVERT: H 130 TYR cc_start: 0.8452 (m-80) cc_final: 0.7999 (m-80) REVERT: L 63 GLN cc_start: 0.8888 (tt0) cc_final: 0.8616 (tt0) outliers start: 9 outliers final: 5 residues processed: 86 average time/residue: 1.0263 time to fit residues: 91.9086 Evaluate side-chains 88 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.119529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.076908 restraints weight = 6396.650| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.82 r_work: 0.2899 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4118 Z= 0.332 Angle : 0.630 10.725 5597 Z= 0.318 Chirality : 0.049 0.335 635 Planarity : 0.004 0.041 705 Dihedral : 5.901 46.684 684 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.91 % Allowed : 12.87 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.45 (0.37), residues: 210 loop : 0.05 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 66 HIS 0.003 0.001 HIS H 54 PHE 0.024 0.002 PHE A 175 TYR 0.012 0.001 TYR H 79 ARG 0.005 0.001 ARG L 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 211 ASN cc_start: 0.8815 (t0) cc_final: 0.8605 (t0) REVERT: H 42 LYS cc_start: 0.8931 (ttmm) cc_final: 0.8723 (tttp) REVERT: H 48 LEU cc_start: 0.8607 (tp) cc_final: 0.8221 (tt) REVERT: H 65 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8043 (pt0) REVERT: H 100 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8127 (ttp) REVERT: H 130 TYR cc_start: 0.8631 (m-80) cc_final: 0.8124 (m-80) REVERT: H 132 TYR cc_start: 0.8814 (m-80) cc_final: 0.8574 (m-80) REVERT: H 134 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7709 (tpp) REVERT: L 63 GLN cc_start: 0.8956 (tt0) cc_final: 0.8641 (tt0) outliers start: 17 outliers final: 11 residues processed: 86 average time/residue: 1.0559 time to fit residues: 94.3706 Evaluate side-chains 90 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 54.3591 > 50: distance: 1 - 2: 4.526 distance: 2 - 3: 3.392 distance: 2 - 9: 6.072 distance: 10 - 11: 8.569 distance: 11 - 12: 6.459 distance: 11 - 17: 8.857 distance: 13 - 14: 10.677 distance: 13 - 15: 12.776 distance: 14 - 16: 9.504 distance: 17 - 18: 4.117 distance: 18 - 19: 9.077 distance: 18 - 21: 19.040 distance: 19 - 20: 18.304 distance: 19 - 24: 16.300 distance: 21 - 22: 12.777 distance: 21 - 23: 12.210 distance: 24 - 25: 23.012 distance: 25 - 26: 18.007 distance: 25 - 28: 12.153 distance: 26 - 27: 14.365 distance: 26 - 32: 6.030 distance: 28 - 29: 13.692 distance: 29 - 30: 11.217 distance: 30 - 31: 7.342 distance: 32 - 33: 12.342 distance: 32 - 101: 25.208 distance: 33 - 34: 20.458 distance: 33 - 36: 4.289 distance: 34 - 35: 13.304 distance: 34 - 39: 26.687 distance: 35 - 98: 17.854 distance: 36 - 37: 33.071 distance: 36 - 38: 18.105 distance: 39 - 40: 10.173 distance: 40 - 41: 30.858 distance: 40 - 43: 9.463 distance: 41 - 42: 15.919 distance: 41 - 48: 18.071 distance: 43 - 44: 17.563 distance: 44 - 45: 20.135 distance: 45 - 46: 22.231 distance: 45 - 47: 19.715 distance: 48 - 49: 30.598 distance: 48 - 89: 31.381 distance: 49 - 50: 18.951 distance: 49 - 52: 49.581 distance: 50 - 51: 25.463 distance: 50 - 54: 30.661 distance: 51 - 86: 24.920 distance: 52 - 53: 50.647 distance: 54 - 55: 24.332 distance: 54 - 60: 18.508 distance: 55 - 56: 25.109 distance: 55 - 58: 24.047 distance: 56 - 57: 31.437 distance: 56 - 61: 42.822 distance: 58 - 59: 15.882 distance: 59 - 60: 7.269 distance: 61 - 62: 17.235 distance: 62 - 63: 25.233 distance: 62 - 65: 5.672 distance: 63 - 64: 22.006 distance: 63 - 69: 23.653 distance: 65 - 66: 19.541 distance: 66 - 67: 13.493 distance: 66 - 68: 25.958