Mon 24 Dec 07:49:26 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 2opl-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2opl-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2opl-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opl-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/2opl-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opl-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 07:49:30 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/2opl-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opl-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 253 and 0 Target number of residues in the AU: 253 Target solvent content: 0.6333 Checking the provided sequence file Detected sequence length: 187 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 374 Adjusted target solvent content: 0.46 Input MTZ file: 2opl-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: 19 Cell parameters: 47.200 82.950 95.370 90.000 90.000 90.000 Input sequence file: 2opl-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 2992 target number of atoms Had to go as low as 0.70 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: 62.588 3.400 Wilson plot Bfac: 67.67 5475 reflections ( 99.44 % complete ) and 0 restraints for refining 3303 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3307 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2932 (Rfree = 0.000) for 3303 atoms. Found 24 (24 requested) and removed 25 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.31 3.49 Search for helices and strands: 0 residues in 0 chains, 3369 seeds are put forward NCS extension: 0 residues added, 3369 seeds are put forward Round 1: 173 peptides, 34 chains. Longest chain 9 peptides. Score 0.342 Round 2: 209 peptides, 34 chains. Longest chain 13 peptides. Score 0.490 Round 3: 233 peptides, 33 chains. Longest chain 14 peptides. Score 0.588 Round 4: 222 peptides, 30 chains. Longest chain 17 peptides. Score 0.596 Round 5: 248 peptides, 27 chains. Longest chain 32 peptides. Score 0.706 Taking the results from Round 5 Chains 27, Residues 221, Estimated correctness of the model 59.4 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 5862 restraints for refining 2720 atoms. 4977 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2239 (Rfree = 0.000) for 2720 atoms. Found 16 (20 requested) and removed 18 (10 requested) atoms. Cycle 2: After refmac, R = 0.2027 (Rfree = 0.000) for 2695 atoms. Found 9 (20 requested) and removed 13 (10 requested) atoms. Cycle 3: After refmac, R = 0.2007 (Rfree = 0.000) for 2687 atoms. Found 5 (19 requested) and removed 13 (10 requested) atoms. Cycle 4: After refmac, R = 0.1948 (Rfree = 0.000) for 2677 atoms. Found 2 (19 requested) and removed 10 (10 requested) atoms. Cycle 5: After refmac, R = 0.1848 (Rfree = 0.000) for 2664 atoms. Found 3 (18 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 3.44 Search for helices and strands: 0 residues in 0 chains, 2785 seeds are put forward NCS extension: 66 residues added (1 deleted due to clashes), 2851 seeds are put forward Round 1: 211 peptides, 33 chains. Longest chain 14 peptides. Score 0.513 Round 2: 247 peptides, 30 chains. Longest chain 30 peptides. Score 0.669 Round 3: 253 peptides, 31 chains. Longest chain 23 peptides. Score 0.672 Round 4: 248 peptides, 28 chains. Longest chain 27 peptides. Score 0.695 Round 5: 235 peptides, 26 chains. Longest chain 25 peptides. Score 0.685 Taking the results from Round 4 Chains 29, Residues 220, Estimated correctness of the model 56.6 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 5836 restraints for refining 2719 atoms. 4939 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2265 (Rfree = 0.000) for 2719 atoms. Found 18 (18 requested) and removed 36 (10 requested) atoms. Cycle 7: After refmac, R = 0.2013 (Rfree = 0.000) for 2691 atoms. Found 5 (18 requested) and removed 11 (10 requested) atoms. Cycle 8: After refmac, R = 0.1930 (Rfree = 0.000) for 2677 atoms. Found 4 (18 requested) and removed 12 (10 requested) atoms. Cycle 9: After refmac, R = 0.1918 (Rfree = 0.000) for 2665 atoms. Found 4 (18 requested) and removed 10 (10 requested) atoms. Cycle 10: After refmac, R = 0.1885 (Rfree = 0.000) for 2657 atoms. Found 1 (18 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.32 3.50 Search for helices and strands: 0 residues in 0 chains, 2748 seeds are put forward NCS extension: 14 residues added (7 deleted due to clashes), 2762 seeds are put forward Round 1: 207 peptides, 30 chains. Longest chain 18 peptides. Score 0.545 Round 2: 237 peptides, 33 chains. Longest chain 25 peptides. Score 0.601 Round 3: 247 peptides, 27 chains. Longest chain 30 peptides. Score 0.704 Round 4: 253 peptides, 28 chains. Longest chain 27 peptides. Score 0.707 Round 5: 224 peptides, 24 chains. Longest chain 25 peptides. Score 0.680 Taking the results from Round 4 Chains 31, Residues 225, Estimated correctness of the model 59.7 % 2 chains (21 residues) have been docked in sequence Building loops using Loopy2018 31 chains (225 residues) following loop building 2 chains (21 residues) in sequence following loop building ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 5797 restraints for refining 2720 atoms. 4867 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2289 (Rfree = 0.000) for 2720 atoms. Found 11 (18 requested) and removed 18 (10 requested) atoms. Cycle 12: After refmac, R = 0.2124 (Rfree = 0.000) for 2705 atoms. Found 2 (18 requested) and removed 10 (10 requested) atoms. Cycle 13: After refmac, R = 0.2046 (Rfree = 0.000) for 2694 atoms. Found 2 (17 requested) and removed 10 (10 requested) atoms. Cycle 14: After refmac, R = 0.2099 (Rfree = 0.000) for 2684 atoms. Found 3 (17 requested) and removed 13 (10 requested) atoms. Cycle 15: After refmac, R = 0.2006 (Rfree = 0.000) for 2670 atoms. Found 3 (16 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 3.51 Search for helices and strands: 0 residues in 0 chains, 2754 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 2777 seeds are put forward Round 1: 214 peptides, 29 chains. Longest chain 29 peptides. Score 0.584 Round 2: 224 peptides, 24 chains. Longest chain 32 peptides. Score 0.680 Round 3: 225 peptides, 25 chains. Longest chain 27 peptides. Score 0.671 Round 4: 228 peptides, 29 chains. Longest chain 17 peptides. Score 0.628 Round 5: 232 peptides, 31 chains. Longest chain 22 peptides. Score 0.613 Taking the results from Round 2 Chains 25, Residues 200, Estimated correctness of the model 52.6 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 6155 restraints for refining 2720 atoms. 5355 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2170 (Rfree = 0.000) for 2720 atoms. Found 5 (16 requested) and removed 10 (10 requested) atoms. Cycle 17: After refmac, R = 0.1979 (Rfree = 0.000) for 2710 atoms. Found 1 (16 requested) and removed 10 (10 requested) atoms. Cycle 18: After refmac, R = 0.1914 (Rfree = 0.000) for 2700 atoms. Found 0 (16 requested) and removed 10 (10 requested) atoms. Cycle 19: After refmac, R = 0.1889 (Rfree = 0.000) for 2689 atoms. Found 1 (16 requested) and removed 10 (10 requested) atoms. Cycle 20: After refmac, R = 0.1891 (Rfree = 0.000) for 2680 atoms. Found 2 (16 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.36 3.54 Search for helices and strands: 0 residues in 0 chains, 2760 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2776 seeds are put forward Round 1: 198 peptides, 28 chains. Longest chain 19 peptides. Score 0.545 Round 2: 213 peptides, 24 chains. Longest chain 29 peptides. Score 0.650 Round 3: 212 peptides, 26 chains. Longest chain 25 peptides. Score 0.620 Round 4: 204 peptides, 23 chains. Longest chain 31 peptides. Score 0.637 Round 5: 214 peptides, 22 chains. Longest chain 30 peptides. Score 0.679 Taking the results from Round 5 Chains 27, Residues 192, Estimated correctness of the model 52.3 % 3 chains (41 residues) have been docked in sequence ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 5795 restraints for refining 2720 atoms. 4917 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2168 (Rfree = 0.000) for 2720 atoms. Found 9 (16 requested) and removed 16 (10 requested) atoms. Cycle 22: After refmac, R = 0.2069 (Rfree = 0.000) for 2704 atoms. Found 7 (16 requested) and removed 13 (10 requested) atoms. Cycle 23: After refmac, R = 0.2097 (Rfree = 0.000) for 2694 atoms. Found 12 (16 requested) and removed 12 (10 requested) atoms. Cycle 24: After refmac, R = 0.1992 (Rfree = 0.000) for 2687 atoms. Found 11 (16 requested) and removed 11 (10 requested) atoms. Cycle 25: After refmac, R = 0.1929 (Rfree = 0.000) for 2681 atoms. Found 12 (16 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.31 3.49 Search for helices and strands: 0 residues in 0 chains, 2786 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 2815 seeds are put forward Round 1: 184 peptides, 27 chains. Longest chain 17 peptides. Score 0.510 Round 2: 184 peptides, 25 chains. Longest chain 24 peptides. Score 0.542 Round 3: 197 peptides, 24 chains. Longest chain 22 peptides. Score 0.602 Round 4: 201 peptides, 26 chains. Longest chain 24 peptides. Score 0.585 Round 5: 195 peptides, 24 chains. Longest chain 25 peptides. Score 0.595 Taking the results from Round 3 Chains 24, Residues 173, Estimated correctness of the model 29.3 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 6234 restraints for refining 2720 atoms. 5548 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2065 (Rfree = 0.000) for 2720 atoms. Found 9 (16 requested) and removed 13 (10 requested) atoms. Cycle 27: After refmac, R = 0.2033 (Rfree = 0.000) for 2713 atoms. Found 8 (16 requested) and removed 12 (10 requested) atoms. Cycle 28: After refmac, R = 0.2397 (Rfree = 0.000) for 2707 atoms. Found 16 (16 requested) and removed 10 (10 requested) atoms. Cycle 29: After refmac, R = 0.2055 (Rfree = 0.000) for 2707 atoms. Found 16 (16 requested) and removed 10 (10 requested) atoms. Cycle 30: After refmac, R = 0.2057 (Rfree = 0.000) for 2710 atoms. Found 14 (16 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 3.46 Search for helices and strands: 0 residues in 0 chains, 2793 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 2813 seeds are put forward Round 1: 158 peptides, 28 chains. Longest chain 13 peptides. Score 0.388 Round 2: 192 peptides, 27 chains. Longest chain 14 peptides. Score 0.539 Round 3: 196 peptides, 27 chains. Longest chain 16 peptides. Score 0.553 Round 4: 195 peptides, 24 chains. Longest chain 24 peptides. Score 0.595 Round 5: 197 peptides, 27 chains. Longest chain 17 peptides. Score 0.557 Taking the results from Round 4 Chains 26, Residues 171, Estimated correctness of the model 27.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 6136 restraints for refining 2719 atoms. 5439 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2197 (Rfree = 0.000) for 2719 atoms. Found 5 (16 requested) and removed 12 (10 requested) atoms. Cycle 32: After refmac, R = 0.2047 (Rfree = 0.000) for 2702 atoms. Found 5 (16 requested) and removed 11 (10 requested) atoms. Cycle 33: After refmac, R = 0.2120 (Rfree = 0.000) for 2694 atoms. Found 12 (16 requested) and removed 11 (10 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2138 (Rfree = 0.000) for 2692 atoms. Found 8 (16 requested) and removed 10 (10 requested) atoms. Cycle 35: After refmac, R = 0.2345 (Rfree = 0.000) for 2688 atoms. Found 16 (16 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 3.45 Search for helices and strands: 0 residues in 0 chains, 2776 seeds are put forward NCS extension: 8 residues added (4 deleted due to clashes), 2784 seeds are put forward Round 1: 185 peptides, 30 chains. Longest chain 13 peptides. Score 0.464 Round 2: 203 peptides, 27 chains. Longest chain 21 peptides. Score 0.577 Round 3: 216 peptides, 27 chains. Longest chain 19 peptides. Score 0.619 Round 4: 213 peptides, 26 chains. Longest chain 25 peptides. Score 0.623 Round 5: 213 peptides, 25 chains. Longest chain 20 peptides. Score 0.637 Taking the results from Round 5 Chains 25, Residues 188, Estimated correctness of the model 40.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 6227 restraints for refining 2720 atoms. 5500 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2448 (Rfree = 0.000) for 2720 atoms. Found 16 (16 requested) and removed 15 (10 requested) atoms. Cycle 37: After refmac, R = 0.2198 (Rfree = 0.000) for 2711 atoms. Found 16 (16 requested) and removed 13 (10 requested) atoms. Cycle 38: After refmac, R = 0.2191 (Rfree = 0.000) for 2709 atoms. Found 16 (16 requested) and removed 12 (10 requested) atoms. Cycle 39: After refmac, R = 0.1921 (Rfree = 0.000) for 2707 atoms. Found 4 (16 requested) and removed 14 (10 requested) atoms. Cycle 40: After refmac, R = 0.1886 (Rfree = 0.000) for 2696 atoms. Found 4 (16 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.30 3.48 Search for helices and strands: 0 residues in 0 chains, 2772 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2789 seeds are put forward Round 1: 163 peptides, 24 chains. Longest chain 18 peptides. Score 0.481 Round 2: 184 peptides, 22 chains. Longest chain 26 peptides. Score 0.589 Round 3: 186 peptides, 22 chains. Longest chain 21 peptides. Score 0.596 Round 4: 191 peptides, 24 chains. Longest chain 17 peptides. Score 0.582 Round 5: 183 peptides, 20 chains. Longest chain 28 peptides. Score 0.615 Taking the results from Round 5 Chains 22, Residues 163, Estimated correctness of the model 33.5 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 6206 restraints for refining 2708 atoms. 5550 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2292 (Rfree = 0.000) for 2708 atoms. Found 16 (16 requested) and removed 16 (10 requested) atoms. Cycle 42: After refmac, R = 0.2059 (Rfree = 0.000) for 2707 atoms. Found 13 (16 requested) and removed 12 (10 requested) atoms. Cycle 43: After refmac, R = 0.2791 (Rfree = 0.000) for 2708 atoms. Found 16 (16 requested) and removed 16 (10 requested) atoms. Cycle 44: After refmac, R = 0.2073 (Rfree = 0.000) for 2699 atoms. Found 15 (16 requested) and removed 18 (10 requested) atoms. Cycle 45: After refmac, R = 0.1959 (Rfree = 0.000) for 2693 atoms. Found 16 (16 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.23 3.41 Search for helices and strands: 0 residues in 0 chains, 2783 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2797 seeds are put forward Round 1: 151 peptides, 25 chains. Longest chain 16 peptides. Score 0.413 Round 2: 184 peptides, 23 chains. Longest chain 29 peptides. Score 0.574 Round 3: 187 peptides, 25 chains. Longest chain 21 peptides. Score 0.553 Round 4: 179 peptides, 22 chains. Longest chain 29 peptides. Score 0.572 Round 5: 179 peptides, 24 chains. Longest chain 16 peptides. Score 0.541 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 161, Estimated correctness of the model 20.0 % 2 chains (14 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2opl-3_warpNtrace.pdb as input Building loops using Loopy2018 25 chains (161 residues) following loop building 2 chains (14 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5475 reflections ( 99.44 % complete ) and 5891 restraints for refining 2632 atoms. 5237 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2094 (Rfree = 0.000) for 2632 atoms. Found 0 (15 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2120 (Rfree = 0.000) for 2616 atoms. Found 0 (15 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1809 (Rfree = 0.000) for 2599 atoms. Found 0 (15 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1943 (Rfree = 0.000) for 2590 atoms. TimeTaking 33.05