Mon 24 Dec 00:06:04 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 2o1q-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2o1q-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2o1q-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o1q-3.4-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/2o1q-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o1q-3.4-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 00:06:09 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/2o1q-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o1q-3.4-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 178 and 0 Target number of residues in the AU: 178 Target solvent content: 0.6231 Checking the provided sequence file Detected sequence length: 145 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 290 Adjusted target solvent content: 0.39 Input MTZ file: 2o1q-3.4-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: 92 Cell parameters: 61.883 61.883 133.475 90.000 90.000 90.000 Input sequence file: 2o1q-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2320 target number of atoms Had to go as low as 0.65 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: 56.142 3.400 Wilson plot Bfac: 62.14 3929 reflections ( 99.75 % complete ) and 0 restraints for refining 2574 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3267 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2797 (Rfree = 0.000) for 2574 atoms. Found 19 (19 requested) and removed 26 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.27 3.80 Search for helices and strands: 0 residues in 0 chains, 2594 seeds are put forward NCS extension: 0 residues added, 2594 seeds are put forward Round 1: 116 peptides, 23 chains. Longest chain 10 peptides. Score 0.334 Round 2: 155 peptides, 25 chains. Longest chain 15 peptides. Score 0.514 Round 3: 158 peptides, 25 chains. Longest chain 11 peptides. Score 0.529 Round 4: 171 peptides, 23 chains. Longest chain 17 peptides. Score 0.631 Round 5: 166 peptides, 22 chains. Longest chain 22 peptides. Score 0.628 Taking the results from Round 4 Chains 25, Residues 148, Estimated correctness of the model 38.5 % 4 chains (28 residues) have been docked in sequence ------------------------------------------------------ 3929 reflections ( 99.75 % complete ) and 4402 restraints for refining 2108 atoms. 3751 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2327 (Rfree = 0.000) for 2108 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 2: After refmac, R = 0.2082 (Rfree = 0.000) for 2081 atoms. Found 7 (15 requested) and removed 9 (7 requested) atoms. Cycle 3: After refmac, R = 0.2011 (Rfree = 0.000) for 2067 atoms. Found 10 (15 requested) and removed 7 (7 requested) atoms. Cycle 4: After refmac, R = 0.1924 (Rfree = 0.000) for 2066 atoms. Found 1 (15 requested) and removed 8 (7 requested) atoms. Cycle 5: After refmac, R = 0.1886 (Rfree = 0.000) for 2058 atoms. Found 3 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.27 3.80 Search for helices and strands: 0 residues in 0 chains, 2100 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 2122 seeds are put forward Round 1: 155 peptides, 26 chains. Longest chain 13 peptides. Score 0.491 Round 2: 168 peptides, 23 chains. Longest chain 19 peptides. Score 0.618 Round 3: 170 peptides, 17 chains. Longest chain 31 peptides. Score 0.730 Round 4: 177 peptides, 20 chains. Longest chain 24 peptides. Score 0.706 Round 5: 176 peptides, 21 chains. Longest chain 22 peptides. Score 0.686 Taking the results from Round 3 Chains 19, Residues 153, Estimated correctness of the model 65.3 % 5 chains (49 residues) have been docked in sequence Building loops using Loopy2018 19 chains (153 residues) following loop building 5 chains (49 residues) in sequence following loop building ------------------------------------------------------ 3929 reflections ( 99.75 % complete ) and 4111 restraints for refining 2109 atoms. 3340 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2168 (Rfree = 0.000) for 2109 atoms. Found 7 (15 requested) and removed 14 (7 requested) atoms. Cycle 7: After refmac, R = 0.1986 (Rfree = 0.000) for 2090 atoms. Found 8 (15 requested) and removed 8 (7 requested) atoms. Cycle 8: After refmac, R = 0.1944 (Rfree = 0.000) for 2085 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. Cycle 9: After refmac, R = 0.1921 (Rfree = 0.000) for 2078 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. Cycle 10: After refmac, R = 0.1898 (Rfree = 0.000) for 2071 atoms. Found 6 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 3.73 Search for helices and strands: 0 residues in 0 chains, 2118 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 2142 seeds are put forward Round 1: 139 peptides, 22 chains. Longest chain 12 peptides. Score 0.497 Round 2: 181 peptides, 24 chains. Longest chain 21 peptides. Score 0.654 Round 3: 166 peptides, 19 chains. Longest chain 21 peptides. Score 0.683 Round 4: 184 peptides, 19 chains. Longest chain 27 peptides. Score 0.744 Round 5: 186 peptides, 18 chains. Longest chain 24 peptides. Score 0.764 Taking the results from Round 5 Chains 22, Residues 168, Estimated correctness of the model 72.8 % 5 chains (54 residues) have been docked in sequence Building loops using Loopy2018 22 chains (168 residues) following loop building 5 chains (54 residues) in sequence following loop building ------------------------------------------------------ 3929 reflections ( 99.75 % complete ) and 4008 restraints for refining 2108 atoms. 3174 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2188 (Rfree = 0.000) for 2108 atoms. Found 13 (13 requested) and removed 12 (7 requested) atoms. Cycle 12: After refmac, R = 0.2058 (Rfree = 0.000) for 2099 atoms. Found 10 (13 requested) and removed 8 (7 requested) atoms. Cycle 13: After refmac, R = 0.1985 (Rfree = 0.000) for 2100 atoms. Found 7 (13 requested) and removed 8 (7 requested) atoms. Cycle 14: After refmac, R = 0.1950 (Rfree = 0.000) for 2097 atoms. Found 2 (13 requested) and removed 7 (7 requested) atoms. Cycle 15: After refmac, R = 0.1926 (Rfree = 0.000) for 2091 atoms. Found 2 (12 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.34 3.88 Search for helices and strands: 0 residues in 0 chains, 2143 seeds are put forward NCS extension: 16 residues added (5 deleted due to clashes), 2159 seeds are put forward Round 1: 144 peptides, 23 chains. Longest chain 12 peptides. Score 0.501 Round 2: 166 peptides, 18 chains. Longest chain 20 peptides. Score 0.700 Round 3: 170 peptides, 21 chains. Longest chain 18 peptides. Score 0.663 Round 4: 162 peptides, 17 chains. Longest chain 19 peptides. Score 0.702 Round 5: 172 peptides, 19 chains. Longest chain 20 peptides. Score 0.705 Taking the results from Round 5 Chains 23, Residues 153, Estimated correctness of the model 59.1 % 4 chains (46 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 67 A and 74 A 20 chains (155 residues) following loop building 3 chains (52 residues) in sequence following loop building ------------------------------------------------------ 3929 reflections ( 99.75 % complete ) and 4261 restraints for refining 2109 atoms. 3483 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2458 (Rfree = 0.000) for 2109 atoms. Found 12 (12 requested) and removed 23 (7 requested) atoms. Cycle 17: After refmac, R = 0.2251 (Rfree = 0.000) for 2089 atoms. Found 12 (12 requested) and removed 8 (7 requested) atoms. Cycle 18: After refmac, R = 0.2068 (Rfree = 0.000) for 2087 atoms. Found 11 (11 requested) and removed 7 (7 requested) atoms. Cycle 19: After refmac, R = 0.2055 (Rfree = 0.000) for 2087 atoms. Found 6 (11 requested) and removed 8 (7 requested) atoms. Cycle 20: After refmac, R = 0.1725 (Rfree = 0.000) for 2080 atoms. Found 5 (11 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 3.80 Search for helices and strands: 0 residues in 0 chains, 2100 seeds are put forward NCS extension: 24 residues added (4 deleted due to clashes), 2124 seeds are put forward Round 1: 140 peptides, 25 chains. Longest chain 18 peptides. Score 0.430 Round 2: 155 peptides, 23 chains. Longest chain 20 peptides. Score 0.558 Round 3: 161 peptides, 24 chains. Longest chain 14 peptides. Score 0.566 Round 4: 162 peptides, 22 chains. Longest chain 14 peptides. Score 0.611 Round 5: 159 peptides, 22 chains. Longest chain 21 peptides. Score 0.598 Taking the results from Round 4 Chains 23, Residues 140, Estimated correctness of the model 32.2 % 4 chains (39 residues) have been docked in sequence ------------------------------------------------------ 3929 reflections ( 99.75 % complete ) and 4475 restraints for refining 2109 atoms. 3818 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2120 (Rfree = 0.000) for 2109 atoms. Found 10 (10 requested) and removed 16 (7 requested) atoms. Cycle 22: After refmac, R = 0.1958 (Rfree = 0.000) for 2095 atoms. Found 6 (10 requested) and removed 8 (7 requested) atoms. Cycle 23: After refmac, R = 0.1905 (Rfree = 0.000) for 2092 atoms. Found 6 (10 requested) and removed 8 (7 requested) atoms. Cycle 24: After refmac, R = 0.1859 (Rfree = 0.000) for 2090 atoms. Found 4 (10 requested) and removed 8 (7 requested) atoms. Cycle 25: After refmac, R = 0.1845 (Rfree = 0.000) for 2085 atoms. Found 3 (10 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.26 3.78 Search for helices and strands: 0 residues in 0 chains, 2116 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2131 seeds are put forward Round 1: 151 peptides, 27 chains. Longest chain 10 peptides. Score 0.445 Round 2: 155 peptides, 20 chains. Longest chain 17 peptides. Score 0.619 Round 3: 142 peptides, 21 chains. Longest chain 18 peptides. Score 0.536 Round 4: 149 peptides, 21 chains. Longest chain 20 peptides. Score 0.571 Round 5: 160 peptides, 23 chains. Longest chain 20 peptides. Score 0.582 Taking the results from Round 2 Chains 22, Residues 135, Estimated correctness of the model 34.8 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 3929 reflections ( 99.75 % complete ) and 4506 restraints for refining 2109 atoms. 3880 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2099 (Rfree = 0.000) for 2109 atoms. Found 8 (10 requested) and removed 19 (7 requested) atoms. Cycle 27: After refmac, R = 0.1933 (Rfree = 0.000) for 2093 atoms. Found 8 (10 requested) and removed 8 (7 requested) atoms. Cycle 28: After refmac, R = 0.1861 (Rfree = 0.000) for 2090 atoms. Found 4 (10 requested) and removed 9 (7 requested) atoms. Cycle 29: After refmac, R = 0.1787 (Rfree = 0.000) for 2084 atoms. Found 2 (10 requested) and removed 8 (7 requested) atoms. Cycle 30: After refmac, R = 0.1737 (Rfree = 0.000) for 2078 atoms. Found 2 (10 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 3.82 Search for helices and strands: 0 residues in 0 chains, 2103 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 2120 seeds are put forward Round 1: 129 peptides, 23 chains. Longest chain 11 peptides. Score 0.415 Round 2: 140 peptides, 21 chains. Longest chain 22 peptides. Score 0.526 Round 3: 149 peptides, 24 chains. Longest chain 13 peptides. Score 0.505 Round 4: 155 peptides, 22 chains. Longest chain 17 peptides. Score 0.579 Round 5: 160 peptides, 24 chains. Longest chain 13 peptides. Score 0.561 Taking the results from Round 4 Chains 23, Residues 133, Estimated correctness of the model 21.7 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3929 reflections ( 99.75 % complete ) and 4737 restraints for refining 2109 atoms. 4203 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2045 (Rfree = 0.000) for 2109 atoms. Found 10 (10 requested) and removed 9 (7 requested) atoms. Cycle 32: After refmac, R = 0.1903 (Rfree = 0.000) for 2107 atoms. Found 2 (10 requested) and removed 7 (7 requested) atoms. Cycle 33: After refmac, R = 0.1870 (Rfree = 0.000) for 2101 atoms. Found 2 (10 requested) and removed 7 (7 requested) atoms. Cycle 34: After refmac, R = 0.1849 (Rfree = 0.000) for 2095 atoms. Found 3 (10 requested) and removed 7 (7 requested) atoms. Cycle 35: After refmac, R = 0.1847 (Rfree = 0.000) for 2091 atoms. Found 1 (10 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.23 3.75 Search for helices and strands: 0 residues in 0 chains, 2119 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 2136 seeds are put forward Round 1: 118 peptides, 20 chains. Longest chain 14 peptides. Score 0.426 Round 2: 122 peptides, 17 chains. Longest chain 16 peptides. Score 0.524 Round 3: 132 peptides, 19 chains. Longest chain 17 peptides. Score 0.530 Round 4: 139 peptides, 19 chains. Longest chain 14 peptides. Score 0.565 Round 5: 134 peptides, 20 chains. Longest chain 13 peptides. Score 0.517 Taking the results from Round 4 Chains 19, Residues 120, Estimated correctness of the model 16.8 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3929 reflections ( 99.75 % complete ) and 4688 restraints for refining 2109 atoms. 4192 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2035 (Rfree = 0.000) for 2109 atoms. Found 4 (10 requested) and removed 8 (7 requested) atoms. Cycle 37: After refmac, R = 0.1973 (Rfree = 0.000) for 2104 atoms. Found 3 (10 requested) and removed 7 (7 requested) atoms. Cycle 38: After refmac, R = 0.1927 (Rfree = 0.000) for 2100 atoms. Found 2 (10 requested) and removed 7 (7 requested) atoms. Cycle 39: After refmac, R = 0.1892 (Rfree = 0.000) for 2095 atoms. Found 1 (10 requested) and removed 7 (7 requested) atoms. Cycle 40: After refmac, R = 0.1882 (Rfree = 0.000) for 2089 atoms. Found 1 (10 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 3.77 Search for helices and strands: 0 residues in 0 chains, 2119 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 2133 seeds are put forward Round 1: 120 peptides, 22 chains. Longest chain 10 peptides. Score 0.386 Round 2: 125 peptides, 20 chains. Longest chain 12 peptides. Score 0.467 Round 3: 124 peptides, 20 chains. Longest chain 12 peptides. Score 0.462 Round 4: 120 peptides, 19 chains. Longest chain 13 peptides. Score 0.464 Round 5: 110 peptides, 18 chains. Longest chain 11 peptides. Score 0.430 Taking the results from Round 2 Chains 20, Residues 105, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 3929 reflections ( 99.75 % complete ) and 4715 restraints for refining 2109 atoms. 4250 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1932 (Rfree = 0.000) for 2109 atoms. Found 10 (10 requested) and removed 8 (7 requested) atoms. Cycle 42: After refmac, R = 0.1861 (Rfree = 0.000) for 2108 atoms. Found 2 (10 requested) and removed 9 (7 requested) atoms. Cycle 43: After refmac, R = 0.1862 (Rfree = 0.000) for 2100 atoms. Found 2 (10 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.1852 (Rfree = 0.000) for 2095 atoms. Found 0 (10 requested) and removed 7 (7 requested) atoms. Cycle 45: After refmac, R = 0.1799 (Rfree = 0.000) for 2087 atoms. Found 2 (10 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.26 3.78 Search for helices and strands: 0 residues in 0 chains, 2121 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2137 seeds are put forward Round 1: 102 peptides, 19 chains. Longest chain 9 peptides. Score 0.353 Round 2: 112 peptides, 18 chains. Longest chain 11 peptides. Score 0.442 Round 3: 113 peptides, 18 chains. Longest chain 12 peptides. Score 0.448 Round 4: 117 peptides, 18 chains. Longest chain 13 peptides. Score 0.471 Round 5: 122 peptides, 17 chains. Longest chain 14 peptides. Score 0.524 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 105, Estimated correctness of the model 1.9 % 1 chains (7 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2o1q-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3929 reflections ( 99.75 % complete ) and 4821 restraints for refining 2109 atoms. 4401 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1795 (Rfree = 0.000) for 2109 atoms. Found 0 (10 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1723 (Rfree = 0.000) for 2095 atoms. Found 0 (10 requested) and removed 4 (7 requested) atoms. Cycle 48: After refmac, R = 0.1728 (Rfree = 0.000) for 2091 atoms. Found 0 (10 requested) and removed 0 (7 requested) atoms. Cycle 49: After refmac, R = 0.1712 (Rfree = 0.000) for 2091 atoms. TimeTaking 28.93