null Sun 23 Dec 23:43:27 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 2p97-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p97-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p97-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p97-3.6-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/2p97-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p97-3.6-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 ============================================================ Sun 23 Dec 23:43:31 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/2p97-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p97-3.6-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 347 and 0 Target number of residues in the AU: 347 Target solvent content: 0.6324 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: 2p97-3.6-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: 2p97-3.6-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 3.600 Wilson plot Bfac: 67.66 6389 reflections ( 99.72 % complete ) and 0 restraints for refining 3572 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3298 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3107 (Rfree = 0.000) for 3572 atoms. Found 22 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.41 3.10 Search for helices and strands: 0 residues in 0 chains, 3648 seeds are put forward NCS extension: 0 residues added, 3648 seeds are put forward Round 1: 220 peptides, 34 chains. Longest chain 22 peptides. Score 0.457 Round 2: 258 peptides, 34 chains. Longest chain 18 peptides. Score 0.561 Round 3: 282 peptides, 33 chains. Longest chain 20 peptides. Score 0.628 Round 4: 285 peptides, 33 chains. Longest chain 24 peptides. Score 0.635 Round 5: 297 peptides, 31 chains. Longest chain 23 peptides. Score 0.678 Taking the results from Round 5 Chains 31, Residues 266, Estimated correctness of the model 42.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 6276 restraints for refining 2914 atoms. 5243 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2833 (Rfree = 0.000) for 2914 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 2: After refmac, R = 0.2683 (Rfree = 0.000) for 2874 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. Cycle 3: After refmac, R = 0.2536 (Rfree = 0.000) for 2864 atoms. Found 8 (18 requested) and removed 11 (9 requested) atoms. Cycle 4: After refmac, R = 0.2450 (Rfree = 0.000) for 2855 atoms. Found 3 (18 requested) and removed 13 (9 requested) atoms. Cycle 5: After refmac, R = 0.2443 (Rfree = 0.000) for 2841 atoms. Found 7 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 3.11 Search for helices and strands: 0 residues in 0 chains, 2931 seeds are put forward NCS extension: 18 residues added (4 deleted due to clashes), 2949 seeds are put forward Round 1: 266 peptides, 27 chains. Longest chain 26 peptides. Score 0.654 Round 2: 280 peptides, 31 chains. Longest chain 26 peptides. Score 0.644 Round 3: 276 peptides, 27 chains. Longest chain 41 peptides. Score 0.674 Round 4: 293 peptides, 26 chains. Longest chain 32 peptides. Score 0.715 Round 5: 284 peptides, 27 chains. Longest chain 29 peptides. Score 0.690 Taking the results from Round 4 Chains 29, Residues 267, Estimated correctness of the model 54.1 % 3 chains (49 residues) have been docked in sequence Building loops using Loopy2018 29 chains (267 residues) following loop building 3 chains (49 residues) in sequence following loop building ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 5693 restraints for refining 2915 atoms. 4477 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2844 (Rfree = 0.000) for 2915 atoms. Found 15 (18 requested) and removed 19 (9 requested) atoms. Cycle 7: After refmac, R = 0.2547 (Rfree = 0.000) for 2892 atoms. Found 14 (18 requested) and removed 14 (9 requested) atoms. Cycle 8: After refmac, R = 0.2375 (Rfree = 0.000) for 2883 atoms. Found 8 (17 requested) and removed 10 (9 requested) atoms. Cycle 9: After refmac, R = 0.2347 (Rfree = 0.000) for 2877 atoms. Found 9 (17 requested) and removed 13 (9 requested) atoms. Cycle 10: After refmac, R = 0.2325 (Rfree = 0.000) for 2865 atoms. Found 7 (17 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.09 Search for helices and strands: 0 residues in 0 chains, 2941 seeds are put forward NCS extension: 20 residues added (10 deleted due to clashes), 2961 seeds are put forward Round 1: 250 peptides, 30 chains. Longest chain 26 peptides. Score 0.586 Round 2: 264 peptides, 25 chains. Longest chain 28 peptides. Score 0.669 Round 3: 267 peptides, 30 chains. Longest chain 27 peptides. Score 0.625 Round 4: 268 peptides, 29 chains. Longest chain 28 peptides. Score 0.638 Round 5: 275 peptides, 23 chains. Longest chain 33 peptides. Score 0.709 Taking the results from Round 5 Chains 26, Residues 252, Estimated correctness of the model 52.3 % 2 chains (42 residues) have been docked in sequence Building loops using Loopy2018 26 chains (252 residues) following loop building 2 chains (42 residues) in sequence following loop building ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 5893 restraints for refining 2916 atoms. 4747 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2558 (Rfree = 0.000) for 2916 atoms. Found 13 (16 requested) and removed 18 (9 requested) atoms. Cycle 12: After refmac, R = 0.2574 (Rfree = 0.000) for 2896 atoms. Found 15 (16 requested) and removed 12 (9 requested) atoms. Cycle 13: After refmac, R = 0.2506 (Rfree = 0.000) for 2881 atoms. Found 8 (15 requested) and removed 12 (9 requested) atoms. Cycle 14: After refmac, R = 0.2427 (Rfree = 0.000) for 2863 atoms. Found 11 (15 requested) and removed 11 (9 requested) atoms. Cycle 15: After refmac, R = 0.2390 (Rfree = 0.000) for 2854 atoms. Found 12 (15 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 3.03 Search for helices and strands: 0 residues in 0 chains, 2936 seeds are put forward NCS extension: 41 residues added (4 deleted due to clashes), 2977 seeds are put forward Round 1: 248 peptides, 32 chains. Longest chain 20 peptides. Score 0.558 Round 2: 255 peptides, 27 chains. Longest chain 25 peptides. Score 0.630 Round 3: 270 peptides, 31 chains. Longest chain 19 peptides. Score 0.622 Round 4: 274 peptides, 30 chains. Longest chain 28 peptides. Score 0.641 Round 5: 255 peptides, 30 chains. Longest chain 29 peptides. Score 0.598 Taking the results from Round 4 Chains 30, Residues 244, Estimated correctness of the model 30.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 6425 restraints for refining 2915 atoms. 5479 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2889 (Rfree = 0.000) for 2915 atoms. Found 14 (14 requested) and removed 29 (9 requested) atoms. Cycle 17: After refmac, R = 0.2480 (Rfree = 0.000) for 2886 atoms. Found 14 (14 requested) and removed 10 (9 requested) atoms. Cycle 18: After refmac, R = 0.2313 (Rfree = 0.000) for 2881 atoms. Found 14 (14 requested) and removed 13 (9 requested) atoms. Cycle 19: After refmac, R = 0.2327 (Rfree = 0.000) for 2880 atoms. Found 10 (14 requested) and removed 10 (9 requested) atoms. Cycle 20: After refmac, R = 0.2158 (Rfree = 0.000) for 2872 atoms. Found 7 (14 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 3.08 Search for helices and strands: 0 residues in 0 chains, 2966 seeds are put forward NCS extension: 45 residues added (3 deleted due to clashes), 3011 seeds are put forward Round 1: 215 peptides, 34 chains. Longest chain 11 peptides. Score 0.442 Round 2: 237 peptides, 29 chains. Longest chain 18 peptides. Score 0.565 Round 3: 242 peptides, 31 chains. Longest chain 24 peptides. Score 0.554 Round 4: 243 peptides, 35 chains. Longest chain 16 peptides. Score 0.510 Round 5: 253 peptides, 30 chains. Longest chain 28 peptides. Score 0.593 Taking the results from Round 5 Chains 30, Residues 223, Estimated correctness of the model 11.9 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 6434 restraints for refining 2916 atoms. 5529 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2623 (Rfree = 0.000) for 2916 atoms. Found 14 (14 requested) and removed 10 (9 requested) atoms. Cycle 22: After refmac, R = 0.2560 (Rfree = 0.000) for 2901 atoms. Found 14 (14 requested) and removed 14 (9 requested) atoms. Cycle 23: After refmac, R = 0.2364 (Rfree = 0.000) for 2890 atoms. Found 12 (14 requested) and removed 10 (9 requested) atoms. Cycle 24: After refmac, R = 0.2266 (Rfree = 0.000) for 2889 atoms. Found 10 (14 requested) and removed 10 (9 requested) atoms. Cycle 25: After refmac, R = 0.2027 (Rfree = 0.000) for 2879 atoms. Found 5 (14 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.37 3.07 Search for helices and strands: 0 residues in 0 chains, 2968 seeds are put forward NCS extension: 29 residues added (6 deleted due to clashes), 2997 seeds are put forward Round 1: 229 peptides, 38 chains. Longest chain 12 peptides. Score 0.432 Round 2: 244 peptides, 33 chains. Longest chain 16 peptides. Score 0.536 Round 3: 249 peptides, 33 chains. Longest chain 18 peptides. Score 0.549 Round 4: 242 peptides, 29 chains. Longest chain 25 peptides. Score 0.577 Round 5: 241 peptides, 26 chains. Longest chain 21 peptides. Score 0.608 Taking the results from Round 5 Chains 26, Residues 215, Estimated correctness of the model 17.8 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 6446 restraints for refining 2915 atoms. 5564 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2592 (Rfree = 0.000) for 2915 atoms. Found 14 (14 requested) and removed 11 (9 requested) atoms. Cycle 27: After refmac, R = 0.2392 (Rfree = 0.000) for 2903 atoms. Found 14 (14 requested) and removed 10 (9 requested) atoms. Cycle 28: After refmac, R = 0.2229 (Rfree = 0.000) for 2899 atoms. Found 9 (14 requested) and removed 10 (9 requested) atoms. Cycle 29: After refmac, R = 0.2220 (Rfree = 0.000) for 2891 atoms. Found 11 (14 requested) and removed 12 (9 requested) atoms. Cycle 30: After refmac, R = 0.2177 (Rfree = 0.000) for 2885 atoms. Found 2 (14 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.37 3.07 Search for helices and strands: 0 residues in 0 chains, 2975 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 2998 seeds are put forward Round 1: 231 peptides, 39 chains. Longest chain 16 peptides. Score 0.425 Round 2: 254 peptides, 32 chains. Longest chain 25 peptides. Score 0.573 Round 3: 258 peptides, 31 chains. Longest chain 19 peptides. Score 0.594 Round 4: 252 peptides, 30 chains. Longest chain 18 peptides. Score 0.591 Round 5: 254 peptides, 30 chains. Longest chain 25 peptides. Score 0.595 Taking the results from Round 5 Chains 30, Residues 224, Estimated correctness of the model 12.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 6474 restraints for refining 2916 atoms. 5608 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2541 (Rfree = 0.000) for 2916 atoms. Found 14 (14 requested) and removed 13 (9 requested) atoms. Cycle 32: After refmac, R = 0.2307 (Rfree = 0.000) for 2903 atoms. Found 7 (14 requested) and removed 10 (9 requested) atoms. Cycle 33: After refmac, R = 0.2219 (Rfree = 0.000) for 2895 atoms. Found 6 (14 requested) and removed 9 (9 requested) atoms. Cycle 34: After refmac, R = 0.2199 (Rfree = 0.000) for 2889 atoms. Found 3 (14 requested) and removed 9 (9 requested) atoms. Cycle 35: After refmac, R = 0.2206 (Rfree = 0.000) for 2883 atoms. Found 0 (14 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.41 3.10 Search for helices and strands: 0 residues in 0 chains, 2941 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 2969 seeds are put forward Round 1: 210 peptides, 31 chains. Longest chain 15 peptides. Score 0.466 Round 2: 229 peptides, 26 chains. Longest chain 22 peptides. Score 0.579 Round 3: 223 peptides, 26 chains. Longest chain 20 peptides. Score 0.564 Round 4: 222 peptides, 24 chains. Longest chain 22 peptides. Score 0.585 Round 5: 231 peptides, 26 chains. Longest chain 17 peptides. Score 0.584 Taking the results from Round 4 Chains 26, Residues 198, Estimated correctness of the model 8.7 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 6467 restraints for refining 2916 atoms. 5633 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2547 (Rfree = 0.000) for 2916 atoms. Found 9 (14 requested) and removed 11 (9 requested) atoms. Cycle 37: After refmac, R = 0.2402 (Rfree = 0.000) for 2910 atoms. Found 8 (14 requested) and removed 10 (9 requested) atoms. Cycle 38: After refmac, R = 0.2403 (Rfree = 0.000) for 2905 atoms. Found 3 (14 requested) and removed 10 (9 requested) atoms. Cycle 39: After refmac, R = 0.2444 (Rfree = 0.000) for 2894 atoms. Found 7 (14 requested) and removed 12 (9 requested) atoms. Cycle 40: After refmac, R = 0.2350 (Rfree = 0.000) for 2886 atoms. Found 8 (14 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.01 Search for helices and strands: 0 residues in 0 chains, 2955 seeds are put forward NCS extension: 33 residues added (4 deleted due to clashes), 2988 seeds are put forward Round 1: 197 peptides, 33 chains. Longest chain 16 peptides. Score 0.400 Round 2: 230 peptides, 34 chains. Longest chain 19 peptides. Score 0.486 Round 3: 231 peptides, 33 chains. Longest chain 16 peptides. Score 0.501 Round 4: 244 peptides, 32 chains. Longest chain 25 peptides. Score 0.548 Round 5: 229 peptides, 30 chains. Longest chain 26 peptides. Score 0.532 Taking the results from Round 4 Chains 33, Residues 212, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 6414 restraints for refining 2915 atoms. 5560 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2488 (Rfree = 0.000) for 2915 atoms. Found 14 (14 requested) and removed 12 (9 requested) atoms. Cycle 42: After refmac, R = 0.2329 (Rfree = 0.000) for 2899 atoms. Found 12 (14 requested) and removed 12 (9 requested) atoms. Cycle 43: After refmac, R = 0.2332 (Rfree = 0.000) for 2888 atoms. Found 12 (14 requested) and removed 11 (9 requested) atoms. Cycle 44: After refmac, R = 0.2188 (Rfree = 0.000) for 2882 atoms. Found 9 (14 requested) and removed 12 (9 requested) atoms. Cycle 45: After refmac, R = 0.2103 (Rfree = 0.000) for 2868 atoms. Found 7 (14 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.07 Search for helices and strands: 0 residues in 0 chains, 2942 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 2964 seeds are put forward Round 1: 198 peptides, 36 chains. Longest chain 11 peptides. Score 0.361 Round 2: 223 peptides, 31 chains. Longest chain 18 peptides. Score 0.504 Round 3: 223 peptides, 34 chains. Longest chain 13 peptides. Score 0.466 Round 4: 233 peptides, 29 chains. Longest chain 17 peptides. Score 0.555 Round 5: 222 peptides, 30 chains. Longest chain 15 peptides. Score 0.513 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 204, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2p97-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6389 reflections ( 99.72 % complete ) and 6635 restraints for refining 2916 atoms. 5848 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2274 (Rfree = 0.000) for 2916 atoms. Found 0 (14 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2205 (Rfree = 0.000) for 2904 atoms. Found 0 (14 requested) and removed 8 (9 requested) atoms. Cycle 48: After refmac, R = 0.2263 (Rfree = 0.000) for 2896 atoms. Found 0 (14 requested) and removed 5 (9 requested) atoms. Cycle 49: After refmac, R = 0.2125 (Rfree = 0.000) for 2890 atoms. Found 0 (14 requested) and removed 8 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:22:05 GMT 2018 Job finished. TimeTaking 38.64 Used memory is bytes: 19458248