null Tue 25 Dec 19:27:57 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 2gnr-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gnr-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gnr-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gnr-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/2gnr-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gnr-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 ============================================================ Tue 25 Dec 19:28:07 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/2gnr-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gnr-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 217 and 0 Target number of residues in the AU: 217 Target solvent content: 0.6396 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: 0.52 Input MTZ file: 2gnr-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: 91 Cell parameters: 75.160 75.160 115.370 90.000 90.000 90.000 Input sequence file: 2gnr-3.2-parrot-hancs.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: 75.160 3.200 Wilson plot Bfac: 71.03 5852 reflections ( 99.54 % complete ) and 0 restraints for refining 2573 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3308 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2468 (Rfree = 0.000) for 2573 atoms. Found 18 (23 requested) and removed 22 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 3.15 Search for helices and strands: 0 residues in 0 chains, 2601 seeds are put forward NCS extension: 0 residues added, 2601 seeds are put forward Round 1: 148 peptides, 22 chains. Longest chain 20 peptides. Score 0.485 Round 2: 175 peptides, 21 chains. Longest chain 26 peptides. Score 0.612 Round 3: 188 peptides, 20 chains. Longest chain 25 peptides. Score 0.671 Round 4: 190 peptides, 19 chains. Longest chain 28 peptides. Score 0.691 Round 5: 191 peptides, 18 chains. Longest chain 31 peptides. Score 0.708 Taking the results from Round 5 Chains 18, Residues 173, Estimated correctness of the model 66.9 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5852 reflections ( 99.54 % complete ) and 4371 restraints for refining 2118 atoms. 3647 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2640 (Rfree = 0.000) for 2118 atoms. Found 13 (19 requested) and removed 22 (9 requested) atoms. Cycle 2: After refmac, R = 0.2502 (Rfree = 0.000) for 2093 atoms. Found 9 (18 requested) and removed 12 (9 requested) atoms. Cycle 3: After refmac, R = 0.2471 (Rfree = 0.000) for 2082 atoms. Found 5 (17 requested) and removed 9 (9 requested) atoms. Cycle 4: After refmac, R = 0.2458 (Rfree = 0.000) for 2074 atoms. Found 4 (17 requested) and removed 9 (9 requested) atoms. Cycle 5: After refmac, R = 0.2448 (Rfree = 0.000) for 2068 atoms. Found 0 (17 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 3.19 Search for helices and strands: 0 residues in 0 chains, 2130 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 2153 seeds are put forward Round 1: 180 peptides, 21 chains. Longest chain 29 peptides. Score 0.629 Round 2: 193 peptides, 21 chains. Longest chain 33 peptides. Score 0.672 Round 3: 195 peptides, 15 chains. Longest chain 49 peptides. Score 0.757 Round 4: 196 peptides, 17 chains. Longest chain 35 peptides. Score 0.734 Round 5: 199 peptides, 18 chains. Longest chain 30 peptides. Score 0.730 Taking the results from Round 3 Chains 16, Residues 180, Estimated correctness of the model 76.3 % 2 chains (72 residues) have been docked in sequence Building loops using Loopy2018 16 chains (180 residues) following loop building 2 chains (72 residues) in sequence following loop building ------------------------------------------------------ 5852 reflections ( 99.54 % complete ) and 3788 restraints for refining 2118 atoms. 2792 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2635 (Rfree = 0.000) for 2118 atoms. Found 9 (17 requested) and removed 22 (9 requested) atoms. Cycle 7: After refmac, R = 0.2540 (Rfree = 0.000) for 2079 atoms. Found 9 (16 requested) and removed 9 (9 requested) atoms. Cycle 8: After refmac, R = 0.2469 (Rfree = 0.000) for 2070 atoms. Found 3 (15 requested) and removed 10 (9 requested) atoms. Cycle 9: After refmac, R = 0.2444 (Rfree = 0.000) for 2060 atoms. Found 4 (15 requested) and removed 9 (9 requested) atoms. Cycle 10: After refmac, R = 0.2440 (Rfree = 0.000) for 2055 atoms. Found 3 (15 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.31 3.22 Search for helices and strands: 0 residues in 0 chains, 2080 seeds are put forward NCS extension: 61 residues added (7 deleted due to clashes), 2141 seeds are put forward Round 1: 166 peptides, 19 chains. Longest chain 25 peptides. Score 0.612 Round 2: 180 peptides, 18 chains. Longest chain 25 peptides. Score 0.675 Round 3: 189 peptides, 16 chains. Longest chain 30 peptides. Score 0.729 Round 4: 198 peptides, 16 chains. Longest chain 42 peptides. Score 0.752 Round 5: 194 peptides, 19 chains. Longest chain 24 peptides. Score 0.703 Taking the results from Round 4 Chains 16, Residues 182, Estimated correctness of the model 75.4 % 2 chains (77 residues) have been docked in sequence Building loops using Loopy2018 16 chains (182 residues) following loop building 2 chains (77 residues) in sequence following loop building ------------------------------------------------------ 5852 reflections ( 99.54 % complete ) and 3757 restraints for refining 2118 atoms. 2743 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2763 (Rfree = 0.000) for 2118 atoms. Found 9 (15 requested) and removed 18 (9 requested) atoms. Cycle 12: After refmac, R = 0.2657 (Rfree = 0.000) for 2091 atoms. Found 11 (14 requested) and removed 9 (9 requested) atoms. Cycle 13: After refmac, R = 0.2575 (Rfree = 0.000) for 2088 atoms. Found 5 (14 requested) and removed 9 (9 requested) atoms. Cycle 14: After refmac, R = 0.2518 (Rfree = 0.000) for 2083 atoms. Found 2 (13 requested) and removed 9 (9 requested) atoms. Cycle 15: After refmac, R = 0.2496 (Rfree = 0.000) for 2073 atoms. Found 2 (13 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.28 3.19 Search for helices and strands: 0 residues in 0 chains, 2122 seeds are put forward NCS extension: 44 residues added (15 deleted due to clashes), 2166 seeds are put forward Round 1: 161 peptides, 20 chains. Longest chain 23 peptides. Score 0.576 Round 2: 175 peptides, 19 chains. Longest chain 22 peptides. Score 0.644 Round 3: 179 peptides, 19 chains. Longest chain 29 peptides. Score 0.657 Round 4: 177 peptides, 17 chains. Longest chain 25 peptides. Score 0.680 Round 5: 193 peptides, 16 chains. Longest chain 50 peptides. Score 0.739 Taking the results from Round 5 Chains 18, Residues 177, Estimated correctness of the model 73.0 % 3 chains (50 residues) have been docked in sequence Building loops using Loopy2018 18 chains (177 residues) following loop building 3 chains (50 residues) in sequence following loop building ------------------------------------------------------ 5852 reflections ( 99.54 % complete ) and 4119 restraints for refining 2118 atoms. 3229 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2780 (Rfree = 0.000) for 2118 atoms. Found 11 (13 requested) and removed 18 (9 requested) atoms. Cycle 17: After refmac, R = 0.2599 (Rfree = 0.000) for 2106 atoms. Found 1 (12 requested) and removed 10 (9 requested) atoms. Cycle 18: After refmac, R = 0.2526 (Rfree = 0.000) for 2092 atoms. Found 6 (12 requested) and removed 9 (9 requested) atoms. Cycle 19: After refmac, R = 0.2462 (Rfree = 0.000) for 2084 atoms. Found 2 (12 requested) and removed 9 (9 requested) atoms. Cycle 20: After refmac, R = 0.2416 (Rfree = 0.000) for 2076 atoms. Found 1 (11 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 3.18 Search for helices and strands: 0 residues in 0 chains, 2121 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 2142 seeds are put forward Round 1: 173 peptides, 22 chains. Longest chain 17 peptides. Score 0.588 Round 2: 192 peptides, 18 chains. Longest chain 33 peptides. Score 0.711 Round 3: 195 peptides, 20 chains. Longest chain 27 peptides. Score 0.692 Round 4: 191 peptides, 16 chains. Longest chain 38 peptides. Score 0.734 Round 5: 184 peptides, 19 chains. Longest chain 27 peptides. Score 0.673 Taking the results from Round 4 Chains 19, Residues 175, Estimated correctness of the model 72.1 % 2 chains (53 residues) have been docked in sequence Building loops using Loopy2018 19 chains (175 residues) following loop building 2 chains (53 residues) in sequence following loop building ------------------------------------------------------ 5852 reflections ( 99.54 % complete ) and 3962 restraints for refining 2118 atoms. 3031 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2786 (Rfree = 0.000) for 2118 atoms. Found 10 (11 requested) and removed 21 (9 requested) atoms. Cycle 22: After refmac, R = 0.2602 (Rfree = 0.000) for 2100 atoms. Found 9 (10 requested) and removed 11 (9 requested) atoms. Cycle 23: After refmac, R = 0.2516 (Rfree = 0.000) for 2096 atoms. Found 6 (10 requested) and removed 9 (9 requested) atoms. Cycle 24: After refmac, R = 0.2472 (Rfree = 0.000) for 2091 atoms. Found 1 (10 requested) and removed 9 (9 requested) atoms. Cycle 25: After refmac, R = 0.2456 (Rfree = 0.000) for 2083 atoms. Found 1 (9 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.29 3.20 Search for helices and strands: 0 residues in 0 chains, 2126 seeds are put forward NCS extension: 29 residues added (6 deleted due to clashes), 2155 seeds are put forward Round 1: 166 peptides, 24 chains. Longest chain 14 peptides. Score 0.525 Round 2: 173 peptides, 18 chains. Longest chain 29 peptides. Score 0.652 Round 3: 178 peptides, 19 chains. Longest chain 33 peptides. Score 0.654 Round 4: 183 peptides, 17 chains. Longest chain 33 peptides. Score 0.698 Round 5: 185 peptides, 22 chains. Longest chain 20 peptides. Score 0.631 Taking the results from Round 4 Chains 18, Residues 166, Estimated correctness of the model 64.8 % 2 chains (52 residues) have been docked in sequence ------------------------------------------------------ 5852 reflections ( 99.54 % complete ) and 4100 restraints for refining 2118 atoms. 3225 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2801 (Rfree = 0.000) for 2118 atoms. Found 9 (9 requested) and removed 20 (9 requested) atoms. Cycle 27: After refmac, R = 0.2668 (Rfree = 0.000) for 2092 atoms. Found 9 (9 requested) and removed 12 (9 requested) atoms. Cycle 28: After refmac, R = 0.2621 (Rfree = 0.000) for 2085 atoms. Found 5 (9 requested) and removed 9 (9 requested) atoms. Cycle 29: After refmac, R = 0.2576 (Rfree = 0.000) for 2078 atoms. Found 6 (9 requested) and removed 10 (9 requested) atoms. Cycle 30: After refmac, R = 0.2553 (Rfree = 0.000) for 2074 atoms. Found 4 (9 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 3.20 Search for helices and strands: 0 residues in 0 chains, 2123 seeds are put forward NCS extension: 40 residues added (6 deleted due to clashes), 2163 seeds are put forward Round 1: 164 peptides, 23 chains. Longest chain 30 peptides. Score 0.535 Round 2: 182 peptides, 21 chains. Longest chain 20 peptides. Score 0.636 Round 3: 185 peptides, 21 chains. Longest chain 22 peptides. Score 0.646 Round 4: 169 peptides, 22 chains. Longest chain 22 peptides. Score 0.572 Round 5: 182 peptides, 20 chains. Longest chain 32 peptides. Score 0.651 Taking the results from Round 5 Chains 20, Residues 162, Estimated correctness of the model 54.1 % 1 chains (31 residues) have been docked in sequence ------------------------------------------------------ 5852 reflections ( 99.54 % complete ) and 4354 restraints for refining 2118 atoms. 3577 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2709 (Rfree = 0.000) for 2118 atoms. Found 9 (9 requested) and removed 21 (9 requested) atoms. Cycle 32: After refmac, R = 0.2609 (Rfree = 0.000) for 2102 atoms. Found 7 (9 requested) and removed 10 (9 requested) atoms. Cycle 33: After refmac, R = 0.2545 (Rfree = 0.000) for 2096 atoms. Found 6 (9 requested) and removed 9 (9 requested) atoms. Cycle 34: After refmac, R = 0.2480 (Rfree = 0.000) for 2092 atoms. Found 5 (9 requested) and removed 9 (9 requested) atoms. Cycle 35: After refmac, R = 0.2449 (Rfree = 0.000) for 2087 atoms. Found 3 (9 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.23 3.15 Search for helices and strands: 0 residues in 0 chains, 2136 seeds are put forward NCS extension: 49 residues added (11 deleted due to clashes), 2185 seeds are put forward Round 1: 148 peptides, 22 chains. Longest chain 13 peptides. Score 0.485 Round 2: 173 peptides, 20 chains. Longest chain 23 peptides. Score 0.621 Round 3: 175 peptides, 20 chains. Longest chain 23 peptides. Score 0.628 Round 4: 180 peptides, 19 chains. Longest chain 23 peptides. Score 0.660 Round 5: 188 peptides, 21 chains. Longest chain 25 peptides. Score 0.656 Taking the results from Round 4 Chains 21, Residues 161, Estimated correctness of the model 56.2 % 2 chains (38 residues) have been docked in sequence ------------------------------------------------------ 5852 reflections ( 99.54 % complete ) and 4272 restraints for refining 2118 atoms. 3492 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2639 (Rfree = 0.000) for 2118 atoms. Found 9 (9 requested) and removed 15 (9 requested) atoms. Cycle 37: After refmac, R = 0.2506 (Rfree = 0.000) for 2110 atoms. Found 4 (9 requested) and removed 10 (9 requested) atoms. Cycle 38: After refmac, R = 0.2396 (Rfree = 0.000) for 2101 atoms. Found 4 (9 requested) and removed 10 (9 requested) atoms. Cycle 39: After refmac, R = 0.2376 (Rfree = 0.000) for 2092 atoms. Found 3 (9 requested) and removed 9 (9 requested) atoms. Cycle 40: After refmac, R = 0.2313 (Rfree = 0.000) for 2083 atoms. Found 2 (9 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.27 3.18 Search for helices and strands: 0 residues in 0 chains, 2119 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 2138 seeds are put forward Round 1: 154 peptides, 22 chains. Longest chain 18 peptides. Score 0.511 Round 2: 168 peptides, 20 chains. Longest chain 23 peptides. Score 0.603 Round 3: 166 peptides, 20 chains. Longest chain 19 peptides. Score 0.595 Round 4: 173 peptides, 21 chains. Longest chain 20 peptides. Score 0.604 Round 5: 187 peptides, 21 chains. Longest chain 27 peptides. Score 0.653 Taking the results from Round 5 Chains 21, Residues 166, Estimated correctness of the model 54.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5852 reflections ( 99.54 % complete ) and 4656 restraints for refining 2118 atoms. 4013 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2505 (Rfree = 0.000) for 2118 atoms. Found 2 (9 requested) and removed 9 (9 requested) atoms. Cycle 42: After refmac, R = 0.2403 (Rfree = 0.000) for 2109 atoms. Found 3 (9 requested) and removed 9 (9 requested) atoms. Cycle 43: After refmac, R = 0.2350 (Rfree = 0.000) for 2101 atoms. Found 3 (9 requested) and removed 10 (9 requested) atoms. Cycle 44: After refmac, R = 0.2334 (Rfree = 0.000) for 2092 atoms. Found 2 (9 requested) and removed 9 (9 requested) atoms. Cycle 45: After refmac, R = 0.2313 (Rfree = 0.000) for 2085 atoms. Found 3 (9 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 3.18 Search for helices and strands: 0 residues in 0 chains, 2130 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 2154 seeds are put forward Round 1: 156 peptides, 21 chains. Longest chain 20 peptides. Score 0.539 Round 2: 165 peptides, 17 chains. Longest chain 36 peptides. Score 0.641 Round 3: 171 peptides, 22 chains. Longest chain 22 peptides. Score 0.580 Round 4: 183 peptides, 22 chains. Longest chain 28 peptides. Score 0.624 Round 5: 176 peptides, 19 chains. Longest chain 32 peptides. Score 0.647 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 157, Estimated correctness of the model 53.1 % 2 chains (21 residues) have been docked in sequence Sequence coverage is 13 % Consider running further cycles of model building using 2gnr-3_warpNtrace.pdb as input Building loops using Loopy2018 20 chains (157 residues) following loop building 2 chains (21 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5852 reflections ( 99.54 % complete ) and 4473 restraints for refining 2118 atoms. 3784 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2468 (Rfree = 0.000) for 2118 atoms. Found 0 (9 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2358 (Rfree = 0.000) for 2104 atoms. Found 0 (9 requested) and removed 7 (9 requested) atoms. Cycle 48: After refmac, R = 0.2321 (Rfree = 0.000) for 2096 atoms. Found 0 (9 requested) and removed 1 (9 requested) atoms. Cycle 49: After refmac, R = 0.2292 (Rfree = 0.000) for 2095 atoms. Found 0 (9 requested) and removed 0 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:16:44 GMT 2018 Job finished. TimeTaking 48.78 Used memory is bytes: 22134296