null Mon 24 Dec 08:00:25 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2hq7-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2hq7-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2hq7-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hq7-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2hq7-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hq7-3.4-parrot-noncs ############### 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 08:00:30 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/noncs/ArpWArp/wArpResults/WorkingDir/2hq7-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hq7-3.4-parrot-noncs/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 194 and 0 Target number of residues in the AU: 194 Target solvent content: 0.6293 Checking the provided sequence file Detected sequence length: 146 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 292 Adjusted target solvent content: 0.44 Input MTZ file: 2hq7-3.4-parrot-noncs.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: 5 Cell parameters: 85.850 36.790 97.970 90.000 113.753 90.000 Input sequence file: 2hq7-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 2336 target number of atoms Had to go as low as 0.75 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: 89.671 3.400 Wilson plot Bfac: 66.03 4012 reflections ( 99.41 % complete ) and 0 restraints for refining 2601 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3216 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2754 (Rfree = 0.000) for 2601 atoms. Found 19 (19 requested) and removed 32 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 3.55 Search for helices and strands: 0 residues in 0 chains, 2635 seeds are put forward NCS extension: 0 residues added, 2635 seeds are put forward Round 1: 153 peptides, 29 chains. Longest chain 19 peptides. Score 0.390 Round 2: 176 peptides, 27 chains. Longest chain 17 peptides. Score 0.548 Round 3: 187 peptides, 21 chains. Longest chain 22 peptides. Score 0.695 Round 4: 193 peptides, 22 chains. Longest chain 20 peptides. Score 0.699 Round 5: 203 peptides, 18 chains. Longest chain 22 peptides. Score 0.781 Taking the results from Round 5 Chains 18, Residues 185, Estimated correctness of the model 76.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4510 restraints for refining 2124 atoms. 3788 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2194 (Rfree = 0.000) for 2124 atoms. Found 15 (16 requested) and removed 14 (8 requested) atoms. Cycle 2: After refmac, R = 0.1896 (Rfree = 0.000) for 2095 atoms. Found 4 (16 requested) and removed 10 (8 requested) atoms. Cycle 3: After refmac, R = 0.1961 (Rfree = 0.000) for 2084 atoms. Found 7 (14 requested) and removed 12 (7 requested) atoms. Cycle 4: After refmac, R = 0.1802 (Rfree = 0.000) for 2071 atoms. Found 4 (14 requested) and removed 9 (7 requested) atoms. Cycle 5: After refmac, R = 0.1827 (Rfree = 0.000) for 2060 atoms. Found 2 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 3.53 Search for helices and strands: 0 residues in 0 chains, 2139 seeds are put forward NCS extension: 39 residues added (1 deleted due to clashes), 2178 seeds are put forward Round 1: 155 peptides, 21 chains. Longest chain 17 peptides. Score 0.572 Round 2: 177 peptides, 21 chains. Longest chain 21 peptides. Score 0.660 Round 3: 198 peptides, 21 chains. Longest chain 30 peptides. Score 0.729 Round 4: 181 peptides, 17 chains. Longest chain 42 peptides. Score 0.735 Round 5: 177 peptides, 23 chains. Longest chain 17 peptides. Score 0.626 Taking the results from Round 4 Chains 18, Residues 164, Estimated correctness of the model 66.4 % 2 chains (60 residues) have been docked in sequence Building loops using Loopy2018 18 chains (164 residues) following loop building 2 chains (60 residues) in sequence following loop building ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4084 restraints for refining 2124 atoms. 3217 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2338 (Rfree = 0.000) for 2124 atoms. Found 13 (14 requested) and removed 30 (8 requested) atoms. Cycle 7: After refmac, R = 0.2143 (Rfree = 0.000) for 2095 atoms. Found 7 (13 requested) and removed 10 (7 requested) atoms. Cycle 8: After refmac, R = 0.1940 (Rfree = 0.000) for 2089 atoms. Found 7 (13 requested) and removed 10 (7 requested) atoms. Cycle 9: After refmac, R = 0.1840 (Rfree = 0.000) for 2084 atoms. Found 6 (13 requested) and removed 15 (7 requested) atoms. Cycle 10: After refmac, R = 0.1739 (Rfree = 0.000) for 2073 atoms. Found 5 (12 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.28 3.55 Search for helices and strands: 0 residues in 0 chains, 2146 seeds are put forward NCS extension: 20 residues added (5 deleted due to clashes), 2166 seeds are put forward Round 1: 164 peptides, 22 chains. Longest chain 17 peptides. Score 0.591 Round 2: 170 peptides, 23 chains. Longest chain 18 peptides. Score 0.598 Round 3: 177 peptides, 20 chains. Longest chain 17 peptides. Score 0.676 Round 4: 178 peptides, 22 chains. Longest chain 22 peptides. Score 0.647 Round 5: 165 peptides, 21 chains. Longest chain 24 peptides. Score 0.614 Taking the results from Round 3 Chains 20, Residues 157, Estimated correctness of the model 51.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4804 restraints for refining 2123 atoms. 4196 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1988 (Rfree = 0.000) for 2123 atoms. Found 10 (13 requested) and removed 10 (8 requested) atoms. Cycle 12: After refmac, R = 0.1779 (Rfree = 0.000) for 2120 atoms. Found 1 (13 requested) and removed 15 (8 requested) atoms. Cycle 13: After refmac, R = 0.1725 (Rfree = 0.000) for 2103 atoms. Found 5 (12 requested) and removed 10 (7 requested) atoms. Cycle 14: After refmac, R = 0.1532 (Rfree = 0.000) for 2094 atoms. Found 4 (12 requested) and removed 9 (7 requested) atoms. Cycle 15: After refmac, R = 0.1511 (Rfree = 0.000) for 2089 atoms. Found 6 (12 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.30 3.58 Search for helices and strands: 0 residues in 0 chains, 2153 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 2173 seeds are put forward Round 1: 161 peptides, 25 chains. Longest chain 15 peptides. Score 0.519 Round 2: 174 peptides, 21 chains. Longest chain 25 peptides. Score 0.649 Round 3: 176 peptides, 20 chains. Longest chain 25 peptides. Score 0.673 Round 4: 177 peptides, 20 chains. Longest chain 22 peptides. Score 0.676 Round 5: 174 peptides, 20 chains. Longest chain 24 peptides. Score 0.666 Taking the results from Round 4 Chains 20, Residues 157, Estimated correctness of the model 51.5 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4604 restraints for refining 2124 atoms. 3924 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1883 (Rfree = 0.000) for 2124 atoms. Found 13 (13 requested) and removed 17 (8 requested) atoms. Cycle 17: After refmac, R = 0.1709 (Rfree = 0.000) for 2116 atoms. Found 4 (13 requested) and removed 8 (8 requested) atoms. Cycle 18: After refmac, R = 0.1673 (Rfree = 0.000) for 2110 atoms. Found 0 (12 requested) and removed 7 (7 requested) atoms. Cycle 19: After refmac, R = 0.1672 (Rfree = 0.000) for 2103 atoms. Found 0 (12 requested) and removed 7 (7 requested) atoms. Cycle 20: After refmac, R = 0.1578 (Rfree = 0.000) for 2096 atoms. Found 0 (12 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.57 Search for helices and strands: 0 residues in 0 chains, 2164 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2183 seeds are put forward Round 1: 157 peptides, 25 chains. Longest chain 15 peptides. Score 0.499 Round 2: 172 peptides, 21 chains. Longest chain 25 peptides. Score 0.642 Round 3: 182 peptides, 23 chains. Longest chain 16 peptides. Score 0.645 Round 4: 180 peptides, 23 chains. Longest chain 15 peptides. Score 0.638 Round 5: 172 peptides, 24 chains. Longest chain 15 peptides. Score 0.588 Taking the results from Round 3 Chains 23, Residues 159, Estimated correctness of the model 42.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4676 restraints for refining 2124 atoms. 4063 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1916 (Rfree = 0.000) for 2124 atoms. Found 4 (13 requested) and removed 10 (8 requested) atoms. Cycle 22: After refmac, R = 0.1768 (Rfree = 0.000) for 2111 atoms. Found 4 (12 requested) and removed 11 (7 requested) atoms. Cycle 23: After refmac, R = 0.1652 (Rfree = 0.000) for 2103 atoms. Found 0 (12 requested) and removed 7 (7 requested) atoms. Cycle 24: After refmac, R = 0.1611 (Rfree = 0.000) for 2094 atoms. Found 0 (12 requested) and removed 7 (7 requested) atoms. Cycle 25: After refmac, R = 0.1595 (Rfree = 0.000) for 2086 atoms. Found 2 (12 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.29 3.57 Search for helices and strands: 0 residues in 0 chains, 2159 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2177 seeds are put forward Round 1: 159 peptides, 21 chains. Longest chain 15 peptides. Score 0.589 Round 2: 160 peptides, 20 chains. Longest chain 18 peptides. Score 0.612 Round 3: 166 peptides, 20 chains. Longest chain 17 peptides. Score 0.636 Round 4: 163 peptides, 21 chains. Longest chain 19 peptides. Score 0.606 Round 5: 167 peptides, 23 chains. Longest chain 16 peptides. Score 0.585 Taking the results from Round 3 Chains 20, Residues 146, Estimated correctness of the model 40.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4889 restraints for refining 2124 atoms. 4325 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1837 (Rfree = 0.000) for 2124 atoms. Found 8 (13 requested) and removed 8 (8 requested) atoms. Cycle 27: After refmac, R = 0.1712 (Rfree = 0.000) for 2123 atoms. Found 3 (13 requested) and removed 10 (8 requested) atoms. Cycle 28: After refmac, R = 0.1668 (Rfree = 0.000) for 2115 atoms. Found 3 (12 requested) and removed 7 (7 requested) atoms. Cycle 29: After refmac, R = 0.1632 (Rfree = 0.000) for 2111 atoms. Found 1 (12 requested) and removed 7 (7 requested) atoms. Cycle 30: After refmac, R = 0.1611 (Rfree = 0.000) for 2105 atoms. Found 1 (12 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 3.57 Search for helices and strands: 0 residues in 0 chains, 2167 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2184 seeds are put forward Round 1: 138 peptides, 23 chains. Longest chain 19 peptides. Score 0.446 Round 2: 158 peptides, 21 chains. Longest chain 18 peptides. Score 0.585 Round 3: 156 peptides, 21 chains. Longest chain 17 peptides. Score 0.576 Round 4: 157 peptides, 21 chains. Longest chain 19 peptides. Score 0.580 Round 5: 161 peptides, 21 chains. Longest chain 17 peptides. Score 0.598 Taking the results from Round 5 Chains 22, Residues 140, Estimated correctness of the model 28.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4814 restraints for refining 2124 atoms. 4236 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2026 (Rfree = 0.000) for 2124 atoms. Found 13 (13 requested) and removed 11 (8 requested) atoms. Cycle 32: After refmac, R = 0.1833 (Rfree = 0.000) for 2123 atoms. Found 4 (13 requested) and removed 8 (8 requested) atoms. Cycle 33: After refmac, R = 0.1761 (Rfree = 0.000) for 2118 atoms. Found 0 (12 requested) and removed 7 (7 requested) atoms. Cycle 34: After refmac, R = 0.1736 (Rfree = 0.000) for 2110 atoms. Found 0 (12 requested) and removed 7 (7 requested) atoms. Cycle 35: After refmac, R = 0.1713 (Rfree = 0.000) for 2103 atoms. Found 0 (12 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 3.57 Search for helices and strands: 0 residues in 0 chains, 2160 seeds are put forward NCS extension: 0 residues added, 2160 seeds are put forward Round 1: 132 peptides, 20 chains. Longest chain 22 peptides. Score 0.483 Round 2: 157 peptides, 25 chains. Longest chain 13 peptides. Score 0.499 Round 3: 166 peptides, 19 chains. Longest chain 25 peptides. Score 0.653 Round 4: 159 peptides, 21 chains. Longest chain 22 peptides. Score 0.589 Round 5: 174 peptides, 22 chains. Longest chain 26 peptides. Score 0.632 Taking the results from Round 3 Chains 21, Residues 147, Estimated correctness of the model 45.0 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4581 restraints for refining 2124 atoms. 3943 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1973 (Rfree = 0.000) for 2124 atoms. Found 6 (13 requested) and removed 12 (8 requested) atoms. Cycle 37: After refmac, R = 0.1906 (Rfree = 0.000) for 2112 atoms. Found 5 (12 requested) and removed 11 (7 requested) atoms. Cycle 38: After refmac, R = 0.1734 (Rfree = 0.000) for 2103 atoms. Found 9 (12 requested) and removed 7 (7 requested) atoms. Cycle 39: After refmac, R = 0.1711 (Rfree = 0.000) for 2104 atoms. Found 5 (12 requested) and removed 7 (7 requested) atoms. Cycle 40: After refmac, R = 0.1641 (Rfree = 0.000) for 2102 atoms. Found 5 (12 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 3.52 Search for helices and strands: 0 residues in 0 chains, 2152 seeds are put forward NCS extension: 19 residues added (7 deleted due to clashes), 2171 seeds are put forward Round 1: 149 peptides, 24 chains. Longest chain 16 peptides. Score 0.481 Round 2: 163 peptides, 26 chains. Longest chain 23 peptides. Score 0.508 Round 3: 157 peptides, 21 chains. Longest chain 13 peptides. Score 0.580 Round 4: 151 peptides, 20 chains. Longest chain 35 peptides. Score 0.574 Round 5: 152 peptides, 22 chains. Longest chain 14 peptides. Score 0.538 Taking the results from Round 3 Chains 21, Residues 136, Estimated correctness of the model 22.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4926 restraints for refining 2124 atoms. 4403 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1841 (Rfree = 0.000) for 2124 atoms. Found 11 (13 requested) and removed 10 (8 requested) atoms. Cycle 42: After refmac, R = 0.1702 (Rfree = 0.000) for 2123 atoms. Found 4 (13 requested) and removed 9 (8 requested) atoms. Cycle 43: After refmac, R = 0.1683 (Rfree = 0.000) for 2116 atoms. Found 4 (12 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.1657 (Rfree = 0.000) for 2112 atoms. Found 2 (12 requested) and removed 8 (7 requested) atoms. Cycle 45: After refmac, R = 0.1616 (Rfree = 0.000) for 2106 atoms. Found 1 (12 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.26 3.53 Search for helices and strands: 0 residues in 0 chains, 2161 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 2173 seeds are put forward Round 1: 141 peptides, 25 chains. Longest chain 11 peptides. Score 0.417 Round 2: 162 peptides, 23 chains. Longest chain 16 peptides. Score 0.563 Round 3: 144 peptides, 19 chains. Longest chain 14 peptides. Score 0.562 Round 4: 153 peptides, 21 chains. Longest chain 13 peptides. Score 0.563 Round 5: 154 peptides, 25 chains. Longest chain 12 peptides. Score 0.484 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 132, Estimated correctness of the model 16.1 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2hq7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4012 reflections ( 99.41 % complete ) and 4955 restraints for refining 2124 atoms. 4448 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1774 (Rfree = 0.000) for 2124 atoms. Found 0 (13 requested) and removed 2 (8 requested) atoms. Cycle 47: After refmac, R = 0.1705 (Rfree = 0.000) for 2116 atoms. Found 0 (13 requested) and removed 0 (8 requested) atoms. Cycle 48: After refmac, R = 0.1684 (Rfree = 0.000) for 2115 atoms. Found 0 (12 requested) and removed 1 (7 requested) atoms. Cycle 49: After refmac, R = 0.1681 (Rfree = 0.000) for 2114 atoms. Found 0 (12 requested) and removed 0 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:29:26 GMT 2018 Job finished. TimeTaking 29.02 Used memory is bytes: 16770896