null Tue 25 Dec 19:27:55 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 2opl-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2opl-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2opl-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opl-3.4-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/2opl-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opl-3.4-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 19:28:05 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/2opl-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opl-3.4-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 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-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: 19 Cell parameters: 47.200 82.950 95.370 90.000 90.000 90.000 Input sequence file: 2opl-3.4-parrot-hancs.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 3323 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3185 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2800 (Rfree = 0.000) for 3323 atoms. Found 25 (25 requested) and removed 31 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 3.48 Search for helices and strands: 0 residues in 0 chains, 3387 seeds are put forward NCS extension: 0 residues added, 3387 seeds are put forward Round 1: 175 peptides, 33 chains. Longest chain 11 peptides. Score 0.370 Round 2: 224 peptides, 31 chains. Longest chain 15 peptides. Score 0.588 Round 3: 226 peptides, 30 chains. Longest chain 23 peptides. Score 0.608 Round 4: 253 peptides, 31 chains. Longest chain 25 peptides. Score 0.672 Round 5: 257 peptides, 32 chains. Longest chain 22 peptides. Score 0.671 Taking the results from Round 4 Chains 31, Residues 222, Estimated correctness of the model 50.4 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 5772 restraints for refining 2718 atoms. 4889 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2557 (Rfree = 0.000) for 2718 atoms. Found 17 (20 requested) and removed 19 (10 requested) atoms. Cycle 2: After refmac, R = 0.2258 (Rfree = 0.000) for 2681 atoms. Found 10 (20 requested) and removed 10 (10 requested) atoms. Cycle 3: After refmac, R = 0.2166 (Rfree = 0.000) for 2665 atoms. Found 5 (20 requested) and removed 13 (10 requested) atoms. Cycle 4: After refmac, R = 0.2037 (Rfree = 0.000) for 2650 atoms. Found 8 (20 requested) and removed 12 (10 requested) atoms. Cycle 5: After refmac, R = 0.1996 (Rfree = 0.000) for 2641 atoms. Found 3 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.52 Search for helices and strands: 0 residues in 0 chains, 2754 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 2773 seeds are put forward Round 1: 203 peptides, 30 chains. Longest chain 24 peptides. Score 0.531 Round 2: 226 peptides, 29 chains. Longest chain 19 peptides. Score 0.622 Round 3: 229 peptides, 27 chains. Longest chain 24 peptides. Score 0.657 Round 4: 247 peptides, 31 chains. Longest chain 18 peptides. Score 0.656 Round 5: 251 peptides, 29 chains. Longest chain 25 peptides. Score 0.691 Taking the results from Round 5 Chains 30, Residues 222, Estimated correctness of the model 55.5 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 5979 restraints for refining 2720 atoms. 5067 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2488 (Rfree = 0.000) for 2720 atoms. Found 11 (20 requested) and removed 12 (10 requested) atoms. Cycle 7: After refmac, R = 0.2361 (Rfree = 0.000) for 2705 atoms. Found 12 (20 requested) and removed 13 (10 requested) atoms. Cycle 8: After refmac, R = 0.2252 (Rfree = 0.000) for 2699 atoms. Found 5 (20 requested) and removed 10 (10 requested) atoms. Cycle 9: After refmac, R = 0.2149 (Rfree = 0.000) for 2689 atoms. Found 6 (20 requested) and removed 13 (10 requested) atoms. Cycle 10: After refmac, R = 0.2034 (Rfree = 0.000) for 2673 atoms. Found 6 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.34 3.52 Search for helices and strands: 0 residues in 0 chains, 2772 seeds are put forward NCS extension: 20 residues added (5 deleted due to clashes), 2792 seeds are put forward Round 1: 210 peptides, 31 chains. Longest chain 17 peptides. Score 0.541 Round 2: 246 peptides, 28 chains. Longest chain 22 peptides. Score 0.690 Round 3: 240 peptides, 25 chains. Longest chain 31 peptides. Score 0.709 Round 4: 241 peptides, 25 chains. Longest chain 31 peptides. Score 0.712 Round 5: 251 peptides, 29 chains. Longest chain 20 peptides. Score 0.691 Taking the results from Round 4 Chains 26, Residues 216, Estimated correctness of the model 60.9 % 2 chains (19 residues) have been docked in sequence Building loops using Loopy2018 26 chains (216 residues) following loop building 2 chains (19 residues) in sequence following loop building ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 5875 restraints for refining 2719 atoms. 4967 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2239 (Rfree = 0.000) for 2719 atoms. Found 9 (20 requested) and removed 12 (10 requested) atoms. Cycle 12: After refmac, R = 0.2026 (Rfree = 0.000) for 2704 atoms. Found 2 (20 requested) and removed 12 (10 requested) atoms. Cycle 13: After refmac, R = 0.2027 (Rfree = 0.000) for 2688 atoms. Found 3 (19 requested) and removed 11 (10 requested) atoms. Cycle 14: After refmac, R = 0.2033 (Rfree = 0.000) for 2676 atoms. Found 1 (19 requested) and removed 13 (10 requested) atoms. Cycle 15: After refmac, R = 0.2242 (Rfree = 0.000) for 2663 atoms. Found 17 (18 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.27 3.45 Search for helices and strands: 0 residues in 0 chains, 2762 seeds are put forward NCS extension: 19 residues added (6 deleted due to clashes), 2781 seeds are put forward Round 1: 214 peptides, 29 chains. Longest chain 21 peptides. Score 0.584 Round 2: 237 peptides, 27 chains. Longest chain 21 peptides. Score 0.678 Round 3: 238 peptides, 32 chains. Longest chain 20 peptides. Score 0.618 Round 4: 237 peptides, 25 chains. Longest chain 26 peptides. Score 0.702 Round 5: 238 peptides, 26 chains. Longest chain 25 peptides. Score 0.693 Taking the results from Round 4 Chains 25, Residues 212, Estimated correctness of the model 58.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 6180 restraints for refining 2719 atoms. 5357 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2352 (Rfree = 0.000) for 2719 atoms. Found 14 (18 requested) and removed 39 (10 requested) atoms. Cycle 17: After refmac, R = 0.2275 (Rfree = 0.000) for 2684 atoms. Found 6 (18 requested) and removed 12 (10 requested) atoms. Cycle 18: After refmac, R = 0.2175 (Rfree = 0.000) for 2674 atoms. Found 11 (17 requested) and removed 12 (10 requested) atoms. Cycle 19: After refmac, R = 0.2087 (Rfree = 0.000) for 2660 atoms. Found 11 (17 requested) and removed 13 (10 requested) atoms. Cycle 20: After refmac, R = 0.2366 (Rfree = 0.000) for 2656 atoms. Found 16 (16 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.47 Search for helices and strands: 0 residues in 0 chains, 2760 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 2785 seeds are put forward Round 1: 190 peptides, 32 chains. Longest chain 17 peptides. Score 0.450 Round 2: 222 peptides, 29 chains. Longest chain 23 peptides. Score 0.609 Round 3: 212 peptides, 29 chains. Longest chain 19 peptides. Score 0.577 Round 4: 217 peptides, 28 chains. Longest chain 21 peptides. Score 0.608 Round 5: 213 peptides, 28 chains. Longest chain 23 peptides. Score 0.595 Taking the results from Round 2 Chains 31, Residues 193, Estimated correctness of the model 31.6 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 6141 restraints for refining 2719 atoms. 5363 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2166 (Rfree = 0.000) for 2719 atoms. Found 16 (16 requested) and removed 15 (10 requested) atoms. Cycle 22: After refmac, R = 0.1973 (Rfree = 0.000) for 2714 atoms. Found 6 (16 requested) and removed 13 (10 requested) atoms. Cycle 23: After refmac, R = 0.1914 (Rfree = 0.000) for 2701 atoms. Found 2 (16 requested) and removed 11 (10 requested) atoms. Cycle 24: After refmac, R = 0.1885 (Rfree = 0.000) for 2689 atoms. Found 6 (16 requested) and removed 10 (10 requested) atoms. Cycle 25: After refmac, R = 0.1839 (Rfree = 0.000) for 2685 atoms. Found 2 (16 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 3.51 Search for helices and strands: 0 residues in 0 chains, 2757 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 2771 seeds are put forward Round 1: 178 peptides, 27 chains. Longest chain 19 peptides. Score 0.487 Round 2: 203 peptides, 26 chains. Longest chain 25 peptides. Score 0.592 Round 3: 210 peptides, 26 chains. Longest chain 23 peptides. Score 0.614 Round 4: 213 peptides, 28 chains. Longest chain 18 peptides. Score 0.595 Round 5: 215 peptides, 24 chains. Longest chain 26 peptides. Score 0.656 Taking the results from Round 5 Chains 24, Residues 191, Estimated correctness of the model 45.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 6269 restraints for refining 2720 atoms. 5529 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2127 (Rfree = 0.000) for 2720 atoms. Found 15 (16 requested) and removed 13 (10 requested) atoms. Cycle 27: After refmac, R = 0.1996 (Rfree = 0.000) for 2721 atoms. Found 5 (16 requested) and removed 10 (10 requested) atoms. Cycle 28: After refmac, R = 0.1960 (Rfree = 0.000) for 2714 atoms. Found 6 (16 requested) and removed 11 (10 requested) atoms. Cycle 29: After refmac, R = 0.1938 (Rfree = 0.000) for 2708 atoms. Found 5 (16 requested) and removed 10 (10 requested) atoms. Cycle 30: After refmac, R = 0.1900 (Rfree = 0.000) for 2701 atoms. Found 3 (16 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.33 3.51 Search for helices and strands: 0 residues in 0 chains, 2780 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 2802 seeds are put forward Round 1: 187 peptides, 31 chains. Longest chain 16 peptides. Score 0.455 Round 2: 212 peptides, 29 chains. Longest chain 23 peptides. Score 0.577 Round 3: 219 peptides, 25 chains. Longest chain 25 peptides. Score 0.654 Round 4: 206 peptides, 23 chains. Longest chain 25 peptides. Score 0.643 Round 5: 205 peptides, 25 chains. Longest chain 26 peptides. Score 0.612 Taking the results from Round 3 Chains 25, Residues 194, Estimated correctness of the model 45.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 6213 restraints for refining 2720 atoms. 5462 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2133 (Rfree = 0.000) for 2720 atoms. Found 10 (16 requested) and removed 11 (10 requested) atoms. Cycle 32: After refmac, R = 0.1999 (Rfree = 0.000) for 2709 atoms. Found 11 (16 requested) and removed 11 (10 requested) atoms. Cycle 33: After refmac, R = 0.1889 (Rfree = 0.000) for 2707 atoms. Found 5 (16 requested) and removed 11 (10 requested) atoms. Cycle 34: After refmac, R = 0.1879 (Rfree = 0.000) for 2700 atoms. Found 7 (16 requested) and removed 11 (10 requested) atoms. Cycle 35: After refmac, R = 0.1818 (Rfree = 0.000) for 2695 atoms. Found 4 (16 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.34 3.52 Search for helices and strands: 0 residues in 0 chains, 2766 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 2783 seeds are put forward Round 1: 183 peptides, 29 chains. Longest chain 19 peptides. Score 0.473 Round 2: 188 peptides, 25 chains. Longest chain 25 peptides. Score 0.557 Round 3: 197 peptides, 26 chains. Longest chain 19 peptides. Score 0.572 Round 4: 194 peptides, 25 chains. Longest chain 21 peptides. Score 0.577 Round 5: 198 peptides, 25 chains. Longest chain 25 peptides. Score 0.590 Taking the results from Round 5 Chains 25, Residues 173, Estimated correctness of the model 25.4 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 6179 restraints for refining 2720 atoms. 5453 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2111 (Rfree = 0.000) for 2720 atoms. Found 5 (16 requested) and removed 12 (10 requested) atoms. Cycle 37: After refmac, R = 0.2089 (Rfree = 0.000) for 2706 atoms. Found 7 (16 requested) and removed 10 (10 requested) atoms. Cycle 38: After refmac, R = 0.1993 (Rfree = 0.000) for 2701 atoms. Found 3 (16 requested) and removed 11 (10 requested) atoms. Cycle 39: After refmac, R = 0.2010 (Rfree = 0.000) for 2692 atoms. Found 7 (16 requested) and removed 11 (10 requested) atoms. Cycle 40: After refmac, R = 0.2035 (Rfree = 0.000) for 2687 atoms. Found 8 (16 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.27 3.45 Search for helices and strands: 0 residues in 0 chains, 2749 seeds are put forward NCS extension: 18 residues added (4 deleted due to clashes), 2767 seeds are put forward Round 1: 148 peptides, 26 chains. Longest chain 12 peptides. Score 0.382 Round 2: 171 peptides, 24 chains. Longest chain 20 peptides. Score 0.511 Round 3: 166 peptides, 23 chains. Longest chain 20 peptides. Score 0.509 Round 4: 171 peptides, 23 chains. Longest chain 18 peptides. Score 0.528 Round 5: 164 peptides, 23 chains. Longest chain 20 peptides. Score 0.502 Taking the results from Round 4 Chains 25, Residues 148, Estimated correctness of the model 3.4 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 6138 restraints for refining 2720 atoms. 5450 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2152 (Rfree = 0.000) for 2720 atoms. Found 13 (16 requested) and removed 17 (10 requested) atoms. Cycle 42: After refmac, R = 0.2040 (Rfree = 0.000) for 2710 atoms. Found 9 (16 requested) and removed 13 (10 requested) atoms. Cycle 43: After refmac, R = 0.1872 (Rfree = 0.000) for 2704 atoms. Found 4 (16 requested) and removed 10 (10 requested) atoms. Cycle 44: After refmac, R = 0.2119 (Rfree = 0.000) for 2697 atoms. Found 16 (16 requested) and removed 11 (10 requested) atoms. Cycle 45: After refmac, R = 0.2062 (Rfree = 0.000) for 2699 atoms. Found 16 (16 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 3.48 Search for helices and strands: 0 residues in 0 chains, 2776 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 2790 seeds are put forward Round 1: 148 peptides, 23 chains. Longest chain 16 peptides. Score 0.438 Round 2: 169 peptides, 25 chains. Longest chain 18 peptides. Score 0.487 Round 3: 169 peptides, 21 chains. Longest chain 20 peptides. Score 0.553 Round 4: 169 peptides, 23 chains. Longest chain 21 peptides. Score 0.520 Round 5: 170 peptides, 22 chains. Longest chain 21 peptides. Score 0.541 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 148, Estimated correctness of the model 12.6 % 1 chains (13 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2opl-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5475 reflections ( 99.44 % complete ) and 6244 restraints for refining 2719 atoms. 5621 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2032 (Rfree = 0.000) for 2719 atoms. Found 0 (16 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2034 (Rfree = 0.000) for 2704 atoms. Found 0 (16 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1959 (Rfree = 0.000) for 2693 atoms. Found 0 (16 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1974 (Rfree = 0.000) for 2680 atoms. Found 0 (16 requested) and removed 8 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:14:47 GMT 2018 Job finished. TimeTaking 46.87 Used memory is bytes: 11701168