null Mon 24 Dec 00:15:17 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 2p97-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p97-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p97-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p97-3.4-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/2p97-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p97-3.4-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 00:15:21 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/2p97-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p97-3.4-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 354 and 0 Target number of residues in the AU: 354 Target solvent content: 0.6250 Checking the provided sequence file Detected sequence length: 201 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 402 Adjusted target solvent content: 0.57 Input MTZ file: 2p97-3.4-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: 94 Cell parameters: 103.080 103.080 96.168 90.000 90.000 90.000 Input sequence file: 2p97-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3216 target number of atoms Had to go as low as 0.85 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: 72.889 3.400 Wilson plot Bfac: 63.69 7539 reflections ( 99.76 % complete ) and 0 restraints for refining 3590 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3274 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3060 (Rfree = 0.000) for 3590 atoms. Found 27 (27 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 3.00 Search for helices and strands: 0 residues in 0 chains, 3660 seeds are put forward NCS extension: 0 residues added, 3660 seeds are put forward Round 1: 231 peptides, 38 chains. Longest chain 13 peptides. Score 0.438 Round 2: 279 peptides, 34 chains. Longest chain 25 peptides. Score 0.611 Round 3: 290 peptides, 34 chains. Longest chain 35 peptides. Score 0.636 Round 4: 295 peptides, 29 chains. Longest chain 24 peptides. Score 0.693 Round 5: 302 peptides, 32 chains. Longest chain 27 peptides. Score 0.679 Taking the results from Round 4 Chains 32, Residues 266, Estimated correctness of the model 56.1 % 3 chains (35 residues) have been docked in sequence ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 5743 restraints for refining 2924 atoms. 4582 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2765 (Rfree = 0.000) for 2924 atoms. Found 22 (22 requested) and removed 20 (11 requested) atoms. Cycle 2: After refmac, R = 0.2514 (Rfree = 0.000) for 2890 atoms. Found 15 (22 requested) and removed 13 (11 requested) atoms. Cycle 3: After refmac, R = 0.2474 (Rfree = 0.000) for 2877 atoms. Found 12 (21 requested) and removed 14 (10 requested) atoms. Cycle 4: After refmac, R = 0.2464 (Rfree = 0.000) for 2869 atoms. Found 5 (21 requested) and removed 17 (10 requested) atoms. Cycle 5: After refmac, R = 0.2392 (Rfree = 0.000) for 2848 atoms. Found 5 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.32 3.02 Search for helices and strands: 0 residues in 0 chains, 2917 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 2938 seeds are put forward Round 1: 274 peptides, 30 chains. Longest chain 29 peptides. Score 0.641 Round 2: 297 peptides, 30 chains. Longest chain 25 peptides. Score 0.688 Round 3: 292 peptides, 29 chains. Longest chain 27 peptides. Score 0.687 Round 4: 296 peptides, 30 chains. Longest chain 24 peptides. Score 0.686 Round 5: 304 peptides, 25 chains. Longest chain 42 peptides. Score 0.742 Taking the results from Round 5 Chains 26, Residues 279, Estimated correctness of the model 68.0 % 4 chains (63 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 163 A and 173 A 24 chains (283 residues) following loop building 3 chains (72 residues) in sequence following loop building ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 5441 restraints for refining 2925 atoms. 4126 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2939 (Rfree = 0.000) for 2925 atoms. Found 22 (22 requested) and removed 31 (11 requested) atoms. Cycle 7: After refmac, R = 0.2744 (Rfree = 0.000) for 2896 atoms. Found 22 (22 requested) and removed 18 (11 requested) atoms. Cycle 8: After refmac, R = 0.2671 (Rfree = 0.000) for 2889 atoms. Found 9 (20 requested) and removed 14 (10 requested) atoms. Cycle 9: After refmac, R = 0.2605 (Rfree = 0.000) for 2876 atoms. Found 8 (20 requested) and removed 12 (10 requested) atoms. Cycle 10: After refmac, R = 0.2556 (Rfree = 0.000) for 2871 atoms. Found 2 (19 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.25 2.96 Search for helices and strands: 0 residues in 0 chains, 2940 seeds are put forward NCS extension: 9 residues added (2 deleted due to clashes), 2949 seeds are put forward Round 1: 263 peptides, 36 chains. Longest chain 29 peptides. Score 0.551 Round 2: 291 peptides, 30 chains. Longest chain 35 peptides. Score 0.676 Round 3: 283 peptides, 34 chains. Longest chain 22 peptides. Score 0.620 Round 4: 289 peptides, 30 chains. Longest chain 42 peptides. Score 0.672 Round 5: 282 peptides, 34 chains. Longest chain 23 peptides. Score 0.618 Taking the results from Round 2 Chains 30, Residues 261, Estimated correctness of the model 51.5 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 6058 restraints for refining 2924 atoms. 4996 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2563 (Rfree = 0.000) for 2924 atoms. Found 19 (20 requested) and removed 14 (11 requested) atoms. Cycle 12: After refmac, R = 0.2417 (Rfree = 0.000) for 2915 atoms. Found 7 (20 requested) and removed 12 (11 requested) atoms. Cycle 13: After refmac, R = 0.2399 (Rfree = 0.000) for 2904 atoms. Found 4 (19 requested) and removed 10 (10 requested) atoms. Cycle 14: After refmac, R = 0.2390 (Rfree = 0.000) for 2890 atoms. Found 6 (19 requested) and removed 10 (10 requested) atoms. Cycle 15: After refmac, R = 0.2348 (Rfree = 0.000) for 2881 atoms. Found 1 (19 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.28 2.99 Search for helices and strands: 0 residues in 0 chains, 2964 seeds are put forward NCS extension: 19 residues added (5 deleted due to clashes), 2983 seeds are put forward Round 1: 245 peptides, 33 chains. Longest chain 18 peptides. Score 0.539 Round 2: 277 peptides, 34 chains. Longest chain 28 peptides. Score 0.606 Round 3: 271 peptides, 35 chains. Longest chain 16 peptides. Score 0.582 Round 4: 281 peptides, 32 chains. Longest chain 32 peptides. Score 0.636 Round 5: 282 peptides, 29 chains. Longest chain 21 peptides. Score 0.667 Taking the results from Round 5 Chains 30, Residues 253, Estimated correctness of the model 49.0 % 3 chains (43 residues) have been docked in sequence ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 5876 restraints for refining 2924 atoms. 4741 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2770 (Rfree = 0.000) for 2924 atoms. Found 17 (20 requested) and removed 17 (11 requested) atoms. Cycle 17: After refmac, R = 0.2509 (Rfree = 0.000) for 2914 atoms. Found 7 (20 requested) and removed 11 (11 requested) atoms. Cycle 18: After refmac, R = 0.2472 (Rfree = 0.000) for 2892 atoms. Found 5 (19 requested) and removed 11 (10 requested) atoms. Cycle 19: After refmac, R = 0.2354 (Rfree = 0.000) for 2871 atoms. Found 3 (19 requested) and removed 12 (10 requested) atoms. Cycle 20: After refmac, R = 0.2319 (Rfree = 0.000) for 2856 atoms. Found 6 (19 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.24 2.95 Search for helices and strands: 0 residues in 0 chains, 2927 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 2953 seeds are put forward Round 1: 265 peptides, 32 chains. Longest chain 18 peptides. Score 0.600 Round 2: 272 peptides, 31 chains. Longest chain 20 peptides. Score 0.626 Round 3: 273 peptides, 29 chains. Longest chain 25 peptides. Score 0.649 Round 4: 267 peptides, 29 chains. Longest chain 22 peptides. Score 0.636 Round 5: 289 peptides, 28 chains. Longest chain 38 peptides. Score 0.690 Taking the results from Round 5 Chains 31, Residues 261, Estimated correctness of the model 55.3 % 4 chains (47 residues) have been docked in sequence ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 5780 restraints for refining 2925 atoms. 4592 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2676 (Rfree = 0.000) for 2925 atoms. Found 12 (20 requested) and removed 14 (11 requested) atoms. Cycle 22: After refmac, R = 0.2496 (Rfree = 0.000) for 2915 atoms. Found 6 (20 requested) and removed 12 (11 requested) atoms. Cycle 23: After refmac, R = 0.2439 (Rfree = 0.000) for 2908 atoms. Found 7 (19 requested) and removed 10 (10 requested) atoms. Cycle 24: After refmac, R = 0.2412 (Rfree = 0.000) for 2902 atoms. Found 5 (19 requested) and removed 10 (10 requested) atoms. Cycle 25: After refmac, R = 0.2376 (Rfree = 0.000) for 2890 atoms. Found 7 (19 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 2.99 Search for helices and strands: 0 residues in 0 chains, 2952 seeds are put forward NCS extension: 0 residues added, 2952 seeds are put forward Round 1: 262 peptides, 36 chains. Longest chain 16 peptides. Score 0.548 Round 2: 287 peptides, 33 chains. Longest chain 25 peptides. Score 0.639 Round 3: 265 peptides, 35 chains. Longest chain 20 peptides. Score 0.567 Round 4: 275 peptides, 28 chains. Longest chain 30 peptides. Score 0.663 Round 5: 286 peptides, 27 chains. Longest chain 28 peptides. Score 0.694 Taking the results from Round 5 Chains 30, Residues 259, Estimated correctness of the model 56.3 % 3 chains (48 residues) have been docked in sequence ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 5634 restraints for refining 2925 atoms. 4455 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2700 (Rfree = 0.000) for 2925 atoms. Found 13 (20 requested) and removed 12 (11 requested) atoms. Cycle 27: After refmac, R = 0.2530 (Rfree = 0.000) for 2906 atoms. Found 7 (20 requested) and removed 11 (11 requested) atoms. Cycle 28: After refmac, R = 0.2524 (Rfree = 0.000) for 2894 atoms. Found 8 (19 requested) and removed 11 (10 requested) atoms. Cycle 29: After refmac, R = 0.2403 (Rfree = 0.000) for 2887 atoms. Found 9 (19 requested) and removed 13 (10 requested) atoms. Cycle 30: After refmac, R = 0.2336 (Rfree = 0.000) for 2876 atoms. Found 3 (19 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.23 2.94 Search for helices and strands: 0 residues in 0 chains, 2947 seeds are put forward NCS extension: 21 residues added (6 deleted due to clashes), 2968 seeds are put forward Round 1: 237 peptides, 30 chains. Longest chain 19 peptides. Score 0.553 Round 2: 255 peptides, 28 chains. Longest chain 22 peptides. Score 0.619 Round 3: 249 peptides, 27 chains. Longest chain 23 peptides. Score 0.616 Round 4: 269 peptides, 28 chains. Longest chain 23 peptides. Score 0.650 Round 5: 270 peptides, 30 chains. Longest chain 25 peptides. Score 0.632 Taking the results from Round 4 Chains 29, Residues 241, Estimated correctness of the model 44.1 % 2 chains (41 residues) have been docked in sequence ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 5947 restraints for refining 2925 atoms. 4849 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2565 (Rfree = 0.000) for 2925 atoms. Found 18 (20 requested) and removed 20 (11 requested) atoms. Cycle 32: After refmac, R = 0.2369 (Rfree = 0.000) for 2913 atoms. Found 5 (20 requested) and removed 12 (11 requested) atoms. Cycle 33: After refmac, R = 0.2283 (Rfree = 0.000) for 2896 atoms. Found 6 (19 requested) and removed 15 (10 requested) atoms. Cycle 34: After refmac, R = 0.2239 (Rfree = 0.000) for 2882 atoms. Found 5 (19 requested) and removed 10 (10 requested) atoms. Cycle 35: After refmac, R = 0.2238 (Rfree = 0.000) for 2874 atoms. Found 6 (19 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.26 2.97 Search for helices and strands: 0 residues in 0 chains, 2913 seeds are put forward NCS extension: 26 residues added (3 deleted due to clashes), 2939 seeds are put forward Round 1: 231 peptides, 32 chains. Longest chain 30 peptides. Score 0.513 Round 2: 265 peptides, 22 chains. Longest chain 38 peptides. Score 0.700 Round 3: 254 peptides, 28 chains. Longest chain 41 peptides. Score 0.617 Round 4: 270 peptides, 26 chains. Longest chain 28 peptides. Score 0.672 Round 5: 263 peptides, 28 chains. Longest chain 19 peptides. Score 0.637 Taking the results from Round 2 Chains 26, Residues 243, Estimated correctness of the model 57.9 % 4 chains (74 residues) have been docked in sequence ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 5434 restraints for refining 2925 atoms. 4182 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2509 (Rfree = 0.000) for 2925 atoms. Found 15 (20 requested) and removed 20 (11 requested) atoms. Cycle 37: After refmac, R = 0.2383 (Rfree = 0.000) for 2914 atoms. Found 7 (20 requested) and removed 13 (11 requested) atoms. Cycle 38: After refmac, R = 0.2314 (Rfree = 0.000) for 2904 atoms. Found 4 (19 requested) and removed 10 (10 requested) atoms. Cycle 39: After refmac, R = 0.2278 (Rfree = 0.000) for 2893 atoms. Found 4 (19 requested) and removed 11 (10 requested) atoms. Cycle 40: After refmac, R = 0.2270 (Rfree = 0.000) for 2881 atoms. Found 3 (19 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.01 Search for helices and strands: 0 residues in 0 chains, 2950 seeds are put forward NCS extension: 40 residues added (2 deleted due to clashes), 2990 seeds are put forward Round 1: 240 peptides, 30 chains. Longest chain 31 peptides. Score 0.561 Round 2: 251 peptides, 26 chains. Longest chain 33 peptides. Score 0.631 Round 3: 252 peptides, 28 chains. Longest chain 22 peptides. Score 0.612 Round 4: 266 peptides, 25 chains. Longest chain 26 peptides. Score 0.673 Round 5: 267 peptides, 28 chains. Longest chain 27 peptides. Score 0.646 Taking the results from Round 4 Chains 26, Residues 241, Estimated correctness of the model 50.7 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 5960 restraints for refining 2925 atoms. 4898 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2645 (Rfree = 0.000) for 2925 atoms. Found 17 (20 requested) and removed 16 (11 requested) atoms. Cycle 42: After refmac, R = 0.2508 (Rfree = 0.000) for 2920 atoms. Found 6 (20 requested) and removed 11 (11 requested) atoms. Cycle 43: After refmac, R = 0.2469 (Rfree = 0.000) for 2911 atoms. Found 8 (20 requested) and removed 14 (11 requested) atoms. Cycle 44: After refmac, R = 0.2448 (Rfree = 0.000) for 2900 atoms. Found 5 (19 requested) and removed 12 (10 requested) atoms. Cycle 45: After refmac, R = 0.2370 (Rfree = 0.000) for 2889 atoms. Found 5 (19 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 3.00 Search for helices and strands: 0 residues in 0 chains, 2937 seeds are put forward NCS extension: 34 residues added (4 deleted due to clashes), 2971 seeds are put forward Round 1: 232 peptides, 31 chains. Longest chain 24 peptides. Score 0.528 Round 2: 265 peptides, 25 chains. Longest chain 35 peptides. Score 0.671 Round 3: 257 peptides, 27 chains. Longest chain 43 peptides. Score 0.634 Round 4: 257 peptides, 27 chains. Longest chain 35 peptides. Score 0.634 Round 5: 269 peptides, 32 chains. Longest chain 31 peptides. Score 0.609 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 240, Estimated correctness of the model 50.1 % 1 chains (34 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 2p97-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7539 reflections ( 99.76 % complete ) and 5946 restraints for refining 2925 atoms. 4887 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2543 (Rfree = 0.000) for 2925 atoms. Found 0 (20 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2438 (Rfree = 0.000) for 2903 atoms. Found 0 (20 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2383 (Rfree = 0.000) for 2886 atoms. Found 0 (19 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2329 (Rfree = 0.000) for 2872 atoms. Found 0 (19 requested) and removed 10 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:50:57 GMT 2018 Job finished. TimeTaking 35.66 Used memory is bytes: 12341248