Mon 24 Dec 01:03:06 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2pr7-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pr7-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pr7-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pr7-3.2-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2pr7-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pr7-3.2-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 01:03:11 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/mrncs/ArpWArp/wArpResults/WorkingDir/2pr7-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pr7-3.2-parrot-mrncs/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-mrncs.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-mrncs.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 2447 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3041 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2134 (Rfree = 0.000) for 2447 atoms. Found 8 (21 requested) and removed 19 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.19 3.23 Search for helices and strands: 0 residues in 0 chains, 2500 seeds are put forward NCS extension: 0 residues added, 2500 seeds are put forward Round 1: 134 peptides, 26 chains. Longest chain 14 peptides. Score 0.349 Round 2: 154 peptides, 24 chains. Longest chain 10 peptides. Score 0.498 Round 3: 165 peptides, 24 chains. Longest chain 14 peptides. Score 0.548 Round 4: 162 peptides, 23 chains. Longest chain 16 peptides. Score 0.554 Round 5: 166 peptides, 24 chains. Longest chain 16 peptides. Score 0.553 Taking the results from Round 4 Chains 23, Residues 139, Estimated correctness of the model 28.0 % 5 chains (38 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 4098 restraints for refining 2001 atoms. 3433 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2401 (Rfree = 0.000) for 2001 atoms. Found 14 (17 requested) and removed 12 (8 requested) atoms. Cycle 2: After refmac, R = 0.2211 (Rfree = 0.000) for 1990 atoms. Found 5 (17 requested) and removed 8 (8 requested) atoms. Cycle 3: After refmac, R = 0.2132 (Rfree = 0.000) for 1975 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. Cycle 4: After refmac, R = 0.2108 (Rfree = 0.000) for 1964 atoms. Found 4 (17 requested) and removed 10 (8 requested) atoms. Cycle 5: After refmac, R = 0.2206 (Rfree = 0.000) for 1956 atoms. Found 9 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.19 3.23 Search for helices and strands: 0 residues in 0 chains, 2054 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2069 seeds are put forward Round 1: 146 peptides, 23 chains. Longest chain 13 peptides. Score 0.480 Round 2: 156 peptides, 20 chains. Longest chain 17 peptides. Score 0.586 Round 3: 165 peptides, 23 chains. Longest chain 13 peptides. Score 0.567 Round 4: 168 peptides, 21 chains. Longest chain 22 peptides. Score 0.616 Round 5: 157 peptides, 20 chains. Longest chain 16 peptides. Score 0.590 Taking the results from Round 4 Chains 21, Residues 147, Estimated correctness of the model 45.2 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 4289 restraints for refining 1984 atoms. 3708 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2152 (Rfree = 0.000) for 1984 atoms. Found 15 (17 requested) and removed 15 (8 requested) atoms. Cycle 7: After refmac, R = 0.1928 (Rfree = 0.000) for 1978 atoms. Found 3 (17 requested) and removed 9 (8 requested) atoms. Cycle 8: After refmac, R = 0.2036 (Rfree = 0.000) for 1969 atoms. Found 3 (17 requested) and removed 9 (8 requested) atoms. Cycle 9: After refmac, R = 0.1700 (Rfree = 0.000) for 1959 atoms. Found 7 (17 requested) and removed 8 (8 requested) atoms. Cycle 10: After refmac, R = 0.1631 (Rfree = 0.000) for 1955 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.18 3.22 Search for helices and strands: 0 residues in 0 chains, 2026 seeds are put forward NCS extension: 26 residues added (3 deleted due to clashes), 2052 seeds are put forward Round 1: 156 peptides, 23 chains. Longest chain 17 peptides. Score 0.527 Round 2: 166 peptides, 22 chains. Longest chain 16 peptides. Score 0.590 Round 3: 167 peptides, 22 chains. Longest chain 19 peptides. Score 0.594 Round 4: 163 peptides, 22 chains. Longest chain 18 peptides. Score 0.578 Round 5: 162 peptides, 21 chains. Longest chain 18 peptides. Score 0.592 Taking the results from Round 3 Chains 22, Residues 145, Estimated correctness of the model 39.4 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 4274 restraints for refining 2000 atoms. 3668 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2027 (Rfree = 0.000) for 2000 atoms. Found 12 (17 requested) and removed 9 (8 requested) atoms. Cycle 12: After refmac, R = 0.1837 (Rfree = 0.000) for 2000 atoms. Found 7 (17 requested) and removed 9 (8 requested) atoms. Cycle 13: After refmac, R = 0.1801 (Rfree = 0.000) for 1998 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. Cycle 14: After refmac, R = 0.1849 (Rfree = 0.000) for 1988 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. Cycle 15: After refmac, R = 0.1779 (Rfree = 0.000) for 1981 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.16 3.20 Search for helices and strands: 0 residues in 0 chains, 2042 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 2060 seeds are put forward Round 1: 146 peptides, 27 chains. Longest chain 11 peptides. Score 0.392 Round 2: 164 peptides, 24 chains. Longest chain 19 peptides. Score 0.544 Round 3: 149 peptides, 20 chains. Longest chain 18 peptides. Score 0.556 Round 4: 151 peptides, 21 chains. Longest chain 21 peptides. Score 0.545 Round 5: 153 peptides, 18 chains. Longest chain 21 peptides. Score 0.611 Taking the results from Round 5 Chains 20, Residues 135, Estimated correctness of the model 43.9 % 4 chains (33 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 4124 restraints for refining 2001 atoms. 3488 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2139 (Rfree = 0.000) for 2001 atoms. Found 11 (17 requested) and removed 13 (8 requested) atoms. Cycle 17: After refmac, R = 0.1962 (Rfree = 0.000) for 1996 atoms. Found 2 (17 requested) and removed 9 (8 requested) atoms. Cycle 18: After refmac, R = 0.1872 (Rfree = 0.000) for 1986 atoms. Found 6 (17 requested) and removed 8 (8 requested) atoms. Cycle 19: After refmac, R = 0.1862 (Rfree = 0.000) for 1982 atoms. Found 5 (17 requested) and removed 8 (8 requested) atoms. Cycle 20: After refmac, R = 0.1830 (Rfree = 0.000) for 1974 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.16 3.20 Search for helices and strands: 0 residues in 0 chains, 2035 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 2054 seeds are put forward Round 1: 134 peptides, 23 chains. Longest chain 11 peptides. Score 0.419 Round 2: 141 peptides, 20 chains. Longest chain 21 peptides. Score 0.519 Round 3: 155 peptides, 22 chains. Longest chain 18 peptides. Score 0.543 Round 4: 156 peptides, 20 chains. Longest chain 25 peptides. Score 0.586 Round 5: 142 peptides, 22 chains. Longest chain 15 peptides. Score 0.482 Taking the results from Round 4 Chains 22, Residues 136, Estimated correctness of the model 37.2 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 4218 restraints for refining 2001 atoms. 3631 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2108 (Rfree = 0.000) for 2001 atoms. Found 7 (17 requested) and removed 9 (8 requested) atoms. Cycle 22: After refmac, R = 0.1996 (Rfree = 0.000) for 1995 atoms. Found 1 (17 requested) and removed 9 (8 requested) atoms. Cycle 23: After refmac, R = 0.1936 (Rfree = 0.000) for 1983 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. Cycle 24: After refmac, R = 0.1891 (Rfree = 0.000) for 1973 atoms. Found 1 (17 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.1865 (Rfree = 0.000) for 1966 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 3.21 Search for helices and strands: 0 residues in 0 chains, 2028 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2044 seeds are put forward Round 1: 139 peptides, 25 chains. Longest chain 11 peptides. Score 0.400 Round 2: 144 peptides, 22 chains. Longest chain 13 peptides. Score 0.491 Round 3: 152 peptides, 20 chains. Longest chain 30 peptides. Score 0.569 Round 4: 155 peptides, 20 chains. Longest chain 14 peptides. Score 0.582 Round 5: 143 peptides, 19 chains. Longest chain 24 peptides. Score 0.549 Taking the results from Round 4 Chains 20, Residues 135, Estimated correctness of the model 36.1 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 4340 restraints for refining 1991 atoms. 3799 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2016 (Rfree = 0.000) for 1991 atoms. Found 9 (17 requested) and removed 9 (8 requested) atoms. Cycle 27: After refmac, R = 0.2124 (Rfree = 0.000) for 1987 atoms. Found 7 (17 requested) and removed 8 (8 requested) atoms. Cycle 28: After refmac, R = 0.1909 (Rfree = 0.000) for 1985 atoms. Found 5 (17 requested) and removed 8 (8 requested) atoms. Cycle 29: After refmac, R = 0.1944 (Rfree = 0.000) for 1980 atoms. Found 4 (17 requested) and removed 9 (8 requested) atoms. Cycle 30: After refmac, R = 0.1995 (Rfree = 0.000) for 1975 atoms. Found 4 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.11 3.15 Search for helices and strands: 0 residues in 0 chains, 2036 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2053 seeds are put forward Round 1: 125 peptides, 21 chains. Longest chain 24 peptides. Score 0.416 Round 2: 134 peptides, 21 chains. Longest chain 23 peptides. Score 0.463 Round 3: 133 peptides, 18 chains. Longest chain 19 peptides. Score 0.524 Round 4: 135 peptides, 17 chains. Longest chain 24 peptides. Score 0.554 Round 5: 133 peptides, 16 chains. Longest chain 29 peptides. Score 0.565 Taking the results from Round 5 Chains 19, Residues 117, Estimated correctness of the model 31.2 % 4 chains (28 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 4206 restraints for refining 2001 atoms. 3651 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2099 (Rfree = 0.000) for 2001 atoms. Found 13 (17 requested) and removed 11 (8 requested) atoms. Cycle 32: After refmac, R = 0.1904 (Rfree = 0.000) for 1993 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. Cycle 33: After refmac, R = 0.1822 (Rfree = 0.000) for 1987 atoms. Found 2 (17 requested) and removed 11 (8 requested) atoms. Cycle 34: After refmac, R = 0.1843 (Rfree = 0.000) for 1976 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. Cycle 35: After refmac, R = 0.1803 (Rfree = 0.000) for 1970 atoms. Found 1 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.14 3.18 Search for helices and strands: 0 residues in 0 chains, 2016 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2031 seeds are put forward Round 1: 132 peptides, 23 chains. Longest chain 12 peptides. Score 0.408 Round 2: 140 peptides, 18 chains. Longest chain 18 peptides. Score 0.556 Round 3: 130 peptides, 19 chains. Longest chain 18 peptides. Score 0.487 Round 4: 138 peptides, 18 chains. Longest chain 16 peptides. Score 0.547 Round 5: 130 peptides, 18 chains. Longest chain 21 peptides. Score 0.509 Taking the results from Round 2 Chains 19, Residues 122, Estimated correctness of the model 28.6 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 4212 restraints for refining 2000 atoms. 3670 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1870 (Rfree = 0.000) for 2000 atoms. Found 9 (17 requested) and removed 10 (8 requested) atoms. Cycle 37: After refmac, R = 0.1853 (Rfree = 0.000) for 1995 atoms. Found 1 (17 requested) and removed 8 (8 requested) atoms. Cycle 38: After refmac, R = 0.1781 (Rfree = 0.000) for 1987 atoms. Found 1 (17 requested) and removed 8 (8 requested) atoms. Cycle 39: After refmac, R = 0.1820 (Rfree = 0.000) for 1980 atoms. Found 5 (17 requested) and removed 8 (8 requested) atoms. Cycle 40: After refmac, R = 0.1800 (Rfree = 0.000) for 1977 atoms. Found 8 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.07 3.11 Search for helices and strands: 0 residues in 0 chains, 2006 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 2027 seeds are put forward Round 1: 98 peptides, 19 chains. Longest chain 12 peptides. Score 0.311 Round 2: 111 peptides, 19 chains. Longest chain 11 peptides. Score 0.387 Round 3: 105 peptides, 16 chains. Longest chain 12 peptides. Score 0.427 Round 4: 104 peptides, 15 chains. Longest chain 12 peptides. Score 0.446 Round 5: 102 peptides, 15 chains. Longest chain 12 peptides. Score 0.435 Taking the results from Round 4 Chains 15, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 4636 restraints for refining 2001 atoms. 4295 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2157 (Rfree = 0.000) for 2001 atoms. Found 9 (17 requested) and removed 10 (8 requested) atoms. Cycle 42: After refmac, R = 0.2078 (Rfree = 0.000) for 1999 atoms. Found 6 (17 requested) and removed 10 (8 requested) atoms. Cycle 43: After refmac, R = 0.1996 (Rfree = 0.000) for 1993 atoms. Found 8 (17 requested) and removed 9 (8 requested) atoms. Cycle 44: After refmac, R = 0.1974 (Rfree = 0.000) for 1989 atoms. Found 6 (17 requested) and removed 9 (8 requested) atoms. Cycle 45: After refmac, R = 0.1883 (Rfree = 0.000) for 1985 atoms. Found 5 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.10 3.14 Search for helices and strands: 0 residues in 0 chains, 2057 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2074 seeds are put forward Round 1: 104 peptides, 20 chains. Longest chain 13 peptides. Score 0.322 Round 2: 115 peptides, 20 chains. Longest chain 11 peptides. Score 0.385 Round 3: 111 peptides, 17 chains. Longest chain 10 peptides. Score 0.435 Round 4: 125 peptides, 20 chains. Longest chain 12 peptides. Score 0.440 Round 5: 123 peptides, 19 chains. Longest chain 13 peptides. Score 0.452 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 104, Estimated correctness of the model 0.0 % 4 chains (17 residues) have been docked in sequence Sequence coverage is 16 % Consider running further cycles of model building using 2pr7-3_warpNtrace.pdb as input Building loops using Loopy2018 19 chains (104 residues) following loop building 4 chains (17 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4512 reflections ( 97.07 % complete ) and 4307 restraints for refining 2001 atoms. 3871 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2247 (Rfree = 0.000) for 2001 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2115 (Rfree = 0.000) for 1988 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1848 (Rfree = 0.000) for 1974 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1664 (Rfree = 0.000) for 1962 atoms. TimeTaking 30.97