null Sun 23 Dec 22:22:41 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2pr7-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pr7-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pr7-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pr7-3.2-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pr7-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pr7-3.2-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:22:50 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pr7-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pr7-3.2-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 198 and 0 Target number of residues in the AU: 198 Target solvent content: 0.6334 Checking the provided sequence file Detected sequence length: 137 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 274 Adjusted target solvent content: 0.49 Input MTZ file: 2pr7-3.2-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 1 Cell parameters: 29.149 45.153 60.777 100.722 103.858 103.308 Input sequence file: 2pr7-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2192 target number of atoms Had to go as low as 0.60 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 57.053 3.201 Wilson plot Bfac: 68.14 4512 reflections ( 97.07 % complete ) and 0 restraints for refining 2432 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3049 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2680 (Rfree = 0.000) for 2432 atoms. Found 19 (21 requested) and removed 28 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.19 3.23 Search for helices and strands: 0 residues in 0 chains, 2480 seeds are put forward NCS extension: 0 residues added, 2480 seeds are put forward Round 1: 145 peptides, 25 chains. Longest chain 12 peptides. Score 0.431 Round 2: 161 peptides, 24 chains. Longest chain 13 peptides. Score 0.530 Round 3: 166 peptides, 25 chains. Longest chain 13 peptides. Score 0.533 Round 4: 171 peptides, 25 chains. Longest chain 14 peptides. Score 0.555 Round 5: 179 peptides, 26 chains. Longest chain 14 peptides. Score 0.571 Taking the results from Round 5 Chains 26, Residues 153, Estimated correctness of the model 32.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 4316 restraints for refining 2001 atoms. 3730 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2308 (Rfree = 0.000) for 2001 atoms. Found 13 (17 requested) and removed 11 (8 requested) atoms. Cycle 2: After refmac, R = 0.2172 (Rfree = 0.000) for 1981 atoms. Found 4 (17 requested) and removed 12 (8 requested) atoms. Cycle 3: After refmac, R = 0.2165 (Rfree = 0.000) for 1963 atoms. Found 5 (17 requested) and removed 9 (8 requested) atoms. Cycle 4: After refmac, R = 0.2168 (Rfree = 0.000) for 1956 atoms. Found 2 (17 requested) and removed 11 (8 requested) atoms. Cycle 5: After refmac, R = 0.2144 (Rfree = 0.000) for 1943 atoms. Found 4 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 3.26 Search for helices and strands: 0 residues in 0 chains, 2030 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 2045 seeds are put forward Round 1: 152 peptides, 24 chains. Longest chain 15 peptides. Score 0.488 Round 2: 159 peptides, 24 chains. Longest chain 12 peptides. Score 0.521 Round 3: 171 peptides, 23 chains. Longest chain 19 peptides. Score 0.593 Round 4: 173 peptides, 23 chains. Longest chain 15 peptides. Score 0.601 Round 5: 190 peptides, 23 chains. Longest chain 21 peptides. Score 0.664 Taking the results from Round 5 Chains 23, Residues 167, Estimated correctness of the model 57.1 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 4056 restraints for refining 2001 atoms. 3332 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2519 (Rfree = 0.000) for 2001 atoms. Found 11 (17 requested) and removed 41 (8 requested) atoms. Cycle 7: After refmac, R = 0.2354 (Rfree = 0.000) for 1964 atoms. Found 2 (17 requested) and removed 19 (8 requested) atoms. Cycle 8: After refmac, R = 0.2325 (Rfree = 0.000) for 1942 atoms. Found 4 (17 requested) and removed 12 (8 requested) atoms. Cycle 9: After refmac, R = 0.2268 (Rfree = 0.000) for 1932 atoms. Found 0 (17 requested) and removed 10 (8 requested) atoms. Cycle 10: After refmac, R = 0.2243 (Rfree = 0.000) for 1921 atoms. Found 1 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 3.26 Search for helices and strands: 0 residues in 0 chains, 1983 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 1986 seeds are put forward Round 1: 141 peptides, 25 chains. Longest chain 10 peptides. Score 0.410 Round 2: 164 peptides, 26 chains. Longest chain 12 peptides. Score 0.504 Round 3: 158 peptides, 23 chains. Longest chain 14 peptides. Score 0.537 Round 4: 166 peptides, 23 chains. Longest chain 15 peptides. Score 0.572 Round 5: 174 peptides, 24 chains. Longest chain 16 peptides. Score 0.587 Taking the results from Round 5 Chains 24, Residues 150, Estimated correctness of the model 37.4 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 4399 restraints for refining 2001 atoms. 3812 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2440 (Rfree = 0.000) for 2001 atoms. Found 9 (17 requested) and removed 36 (8 requested) atoms. Cycle 12: After refmac, R = 0.2512 (Rfree = 0.000) for 1970 atoms. Found 16 (17 requested) and removed 15 (8 requested) atoms. Cycle 13: After refmac, R = 0.2561 (Rfree = 0.000) for 1969 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Cycle 14: After refmac, R = 0.2375 (Rfree = 0.000) for 1958 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 15: After refmac, R = 0.2256 (Rfree = 0.000) for 1948 atoms. Found 16 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.18 3.22 Search for helices and strands: 0 residues in 0 chains, 2048 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2066 seeds are put forward Round 1: 144 peptides, 28 chains. Longest chain 9 peptides. Score 0.358 Round 2: 143 peptides, 24 chains. Longest chain 14 peptides. Score 0.443 Round 3: 158 peptides, 25 chains. Longest chain 17 peptides. Score 0.496 Round 4: 166 peptides, 24 chains. Longest chain 13 peptides. Score 0.553 Round 5: 158 peptides, 21 chains. Longest chain 18 peptides. Score 0.575 Taking the results from Round 5 Chains 23, Residues 137, Estimated correctness of the model 34.1 % 5 chains (28 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 4227 restraints for refining 2001 atoms. 3631 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2266 (Rfree = 0.000) for 2001 atoms. Found 12 (17 requested) and removed 11 (8 requested) atoms. Cycle 17: After refmac, R = 0.2091 (Rfree = 0.000) for 1999 atoms. Found 2 (17 requested) and removed 9 (8 requested) atoms. Cycle 18: After refmac, R = 0.2023 (Rfree = 0.000) for 1983 atoms. Found 4 (17 requested) and removed 10 (8 requested) atoms. Cycle 19: After refmac, R = 0.2016 (Rfree = 0.000) for 1975 atoms. Found 3 (17 requested) and removed 12 (8 requested) atoms. Cycle 20: After refmac, R = 0.1946 (Rfree = 0.000) for 1965 atoms. Found 2 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.17 3.21 Search for helices and strands: 0 residues in 0 chains, 2025 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2039 seeds are put forward Round 1: 143 peptides, 23 chains. Longest chain 16 peptides. Score 0.465 Round 2: 164 peptides, 23 chains. Longest chain 16 peptides. Score 0.563 Round 3: 150 peptides, 22 chains. Longest chain 12 peptides. Score 0.520 Round 4: 157 peptides, 23 chains. Longest chain 18 peptides. Score 0.532 Round 5: 154 peptides, 22 chains. Longest chain 15 peptides. Score 0.538 Taking the results from Round 2 Chains 23, Residues 141, Estimated correctness of the model 30.6 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 4387 restraints for refining 2001 atoms. 3827 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2505 (Rfree = 0.000) for 2001 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 22: After refmac, R = 0.2291 (Rfree = 0.000) for 1991 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 23: After refmac, R = 0.1824 (Rfree = 0.000) for 1988 atoms. Found 9 (17 requested) and removed 8 (8 requested) atoms. Cycle 24: After refmac, R = 0.1711 (Rfree = 0.000) for 1988 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.1701 (Rfree = 0.000) for 1981 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.22 3.26 Search for helices and strands: 0 residues in 0 chains, 2050 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 2067 seeds are put forward Round 1: 135 peptides, 22 chains. Longest chain 18 peptides. Score 0.446 Round 2: 160 peptides, 25 chains. Longest chain 15 peptides. Score 0.506 Round 3: 167 peptides, 23 chains. Longest chain 18 peptides. Score 0.576 Round 4: 170 peptides, 25 chains. Longest chain 12 peptides. Score 0.551 Round 5: 170 peptides, 23 chains. Longest chain 18 peptides. Score 0.588 Taking the results from Round 5 Chains 23, Residues 147, Estimated correctness of the model 37.7 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 4104 restraints for refining 2001 atoms. 3463 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2101 (Rfree = 0.000) for 2001 atoms. Found 14 (17 requested) and removed 15 (8 requested) atoms. Cycle 27: After refmac, R = 0.1883 (Rfree = 0.000) for 1995 atoms. Found 9 (17 requested) and removed 9 (8 requested) atoms. Cycle 28: After refmac, R = 0.1815 (Rfree = 0.000) for 1992 atoms. Found 4 (17 requested) and removed 9 (8 requested) atoms. Cycle 29: After refmac, R = 0.1791 (Rfree = 0.000) for 1986 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. Cycle 30: After refmac, R = 0.1684 (Rfree = 0.000) for 1980 atoms. Found 4 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.21 3.25 Search for helices and strands: 0 residues in 0 chains, 2054 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 2072 seeds are put forward Round 1: 152 peptides, 28 chains. Longest chain 14 peptides. Score 0.401 Round 2: 171 peptides, 26 chains. Longest chain 15 peptides. Score 0.536 Round 3: 180 peptides, 30 chains. Longest chain 12 peptides. Score 0.499 Round 4: 175 peptides, 26 chains. Longest chain 18 peptides. Score 0.554 Round 5: 183 peptides, 26 chains. Longest chain 17 peptides. Score 0.587 Taking the results from Round 5 Chains 28, Residues 157, Estimated correctness of the model 37.4 % 4 chains (22 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 3974 restraints for refining 2001 atoms. 3302 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2193 (Rfree = 0.000) for 2001 atoms. Found 15 (17 requested) and removed 12 (8 requested) atoms. Cycle 32: After refmac, R = 0.1998 (Rfree = 0.000) for 1998 atoms. Found 6 (17 requested) and removed 8 (8 requested) atoms. Cycle 33: After refmac, R = 0.1952 (Rfree = 0.000) for 1990 atoms. Found 4 (17 requested) and removed 8 (8 requested) atoms. Cycle 34: After refmac, R = 0.1939 (Rfree = 0.000) for 1981 atoms. Found 4 (17 requested) and removed 8 (8 requested) atoms. Cycle 35: After refmac, R = 0.1820 (Rfree = 0.000) for 1973 atoms. Found 7 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.20 3.24 Search for helices and strands: 0 residues in 0 chains, 2040 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 2053 seeds are put forward Round 1: 132 peptides, 23 chains. Longest chain 18 peptides. Score 0.408 Round 2: 140 peptides, 20 chains. Longest chain 17 peptides. Score 0.515 Round 3: 148 peptides, 21 chains. Longest chain 18 peptides. Score 0.531 Round 4: 155 peptides, 22 chains. Longest chain 18 peptides. Score 0.543 Round 5: 152 peptides, 22 chains. Longest chain 14 peptides. Score 0.529 Taking the results from Round 4 Chains 26, Residues 133, Estimated correctness of the model 24.7 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 4241 restraints for refining 2001 atoms. 3665 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2088 (Rfree = 0.000) for 2001 atoms. Found 7 (17 requested) and removed 9 (8 requested) atoms. Cycle 37: After refmac, R = 0.1946 (Rfree = 0.000) for 1995 atoms. Found 5 (17 requested) and removed 10 (8 requested) atoms. Cycle 38: After refmac, R = 0.1923 (Rfree = 0.000) for 1989 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. Cycle 39: After refmac, R = 0.2146 (Rfree = 0.000) for 1984 atoms. Found 11 (17 requested) and removed 9 (8 requested) atoms. Cycle 40: After refmac, R = 0.1853 (Rfree = 0.000) for 1985 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.21 3.25 Search for helices and strands: 0 residues in 0 chains, 2038 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2056 seeds are put forward Round 1: 121 peptides, 22 chains. Longest chain 11 peptides. Score 0.371 Round 2: 128 peptides, 18 chains. Longest chain 12 peptides. Score 0.500 Round 3: 146 peptides, 20 chains. Longest chain 13 peptides. Score 0.542 Round 4: 141 peptides, 22 chains. Longest chain 12 peptides. Score 0.477 Round 5: 147 peptides, 22 chains. Longest chain 12 peptides. Score 0.506 Taking the results from Round 3 Chains 20, Residues 126, Estimated correctness of the model 24.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 4534 restraints for refining 2001 atoms. 4050 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2478 (Rfree = 0.000) for 2001 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 42: After refmac, R = 0.2319 (Rfree = 0.000) for 1998 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 43: After refmac, R = 0.1876 (Rfree = 0.000) for 2002 atoms. Found 5 (17 requested) and removed 8 (8 requested) atoms. Cycle 44: After refmac, R = 0.1922 (Rfree = 0.000) for 1994 atoms. Found 7 (17 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.1774 (Rfree = 0.000) for 1992 atoms. Found 7 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 3.22 Search for helices and strands: 0 residues in 0 chains, 2049 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2063 seeds are put forward Round 1: 100 peptides, 20 chains. Longest chain 10 peptides. Score 0.297 Round 2: 111 peptides, 18 chains. Longest chain 12 peptides. Score 0.411 Round 3: 123 peptides, 19 chains. Longest chain 13 peptides. Score 0.452 Round 4: 123 peptides, 17 chains. Longest chain 16 peptides. Score 0.497 Round 5: 133 peptides, 18 chains. Longest chain 17 peptides. Score 0.524 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 115, Estimated correctness of the model 18.9 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2pr7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4512 reflections ( 97.07 % complete ) and 4349 restraints for refining 1980 atoms. 3907 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1942 (Rfree = 0.000) for 1980 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1847 (Rfree = 0.000) for 1968 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1774 (Rfree = 0.000) for 1958 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1727 (Rfree = 0.000) for 1949 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:56:24 GMT 2018 Job finished. TimeTaking 33.72 Used memory is bytes: 18783272