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 2p8j-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p8j-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p8j-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p8j-4.0-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/2p8j-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p8j-4.0-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/2p8j-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p8j-4.0-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 398 and 0 Target number of residues in the AU: 398 Target solvent content: 0.6668 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 418 Adjusted target solvent content: 0.65 Input MTZ file: 2p8j-4.0-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: 152 Cell parameters: 83.860 83.860 159.200 90.000 90.000 120.000 Input sequence file: 2p8j-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3344 target number of atoms Had to go as low as 1.10 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: 72.625 4.000 Wilson plot Bfac: 89.83 5718 reflections ( 98.03 % complete ) and 0 restraints for refining 3686 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3523 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3207 (Rfree = 0.000) for 3686 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.79 3.08 Search for helices and strands: 0 residues in 0 chains, 3773 seeds are put forward NCS extension: 0 residues added, 3773 seeds are put forward Round 1: 208 peptides, 36 chains. Longest chain 13 peptides. Score 0.358 Round 2: 252 peptides, 32 chains. Longest chain 21 peptides. Score 0.509 Round 3: 260 peptides, 31 chains. Longest chain 22 peptides. Score 0.536 Round 4: 267 peptides, 29 chains. Longest chain 30 peptides. Score 0.570 Round 5: 270 peptides, 30 chains. Longest chain 34 peptides. Score 0.567 Taking the results from Round 4 Chains 29, Residues 238, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6827 restraints for refining 3020 atoms. 5904 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2434 (Rfree = 0.000) for 3020 atoms. Found 8 (14 requested) and removed 14 (7 requested) atoms. Cycle 2: After refmac, R = 0.2303 (Rfree = 0.000) for 2974 atoms. Found 7 (14 requested) and removed 13 (7 requested) atoms. Cycle 3: After refmac, R = 0.2281 (Rfree = 0.000) for 2953 atoms. Found 10 (14 requested) and removed 17 (7 requested) atoms. Cycle 4: After refmac, R = 0.2233 (Rfree = 0.000) for 2935 atoms. Found 9 (13 requested) and removed 15 (6 requested) atoms. Cycle 5: After refmac, R = 0.2188 (Rfree = 0.000) for 2926 atoms. Found 7 (13 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.81 3.10 Search for helices and strands: 0 residues in 0 chains, 3042 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3059 seeds are put forward Round 1: 223 peptides, 32 chains. Longest chain 14 peptides. Score 0.442 Round 2: 266 peptides, 32 chains. Longest chain 20 peptides. Score 0.539 Round 3: 261 peptides, 28 chains. Longest chain 18 peptides. Score 0.568 Round 4: 254 peptides, 25 chains. Longest chain 31 peptides. Score 0.582 Round 5: 255 peptides, 22 chains. Longest chain 45 peptides. Score 0.612 Taking the results from Round 5 Chains 24, Residues 233, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6354 restraints for refining 3020 atoms. 5368 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2645 (Rfree = 0.000) for 3020 atoms. Found 13 (14 requested) and removed 12 (7 requested) atoms. Cycle 7: After refmac, R = 0.2562 (Rfree = 0.000) for 2993 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 8: After refmac, R = 0.2480 (Rfree = 0.000) for 2978 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 9: After refmac, R = 0.2502 (Rfree = 0.000) for 2970 atoms. Found 12 (14 requested) and removed 9 (7 requested) atoms. Cycle 10: After refmac, R = 0.2371 (Rfree = 0.000) for 2952 atoms. Found 8 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.77 3.07 Search for helices and strands: 0 residues in 0 chains, 3059 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3077 seeds are put forward Round 1: 240 peptides, 32 chains. Longest chain 24 peptides. Score 0.482 Round 2: 246 peptides, 29 chains. Longest chain 22 peptides. Score 0.526 Round 3: 265 peptides, 31 chains. Longest chain 22 peptides. Score 0.547 Round 4: 270 peptides, 30 chains. Longest chain 28 peptides. Score 0.567 Round 5: 277 peptides, 30 chains. Longest chain 37 peptides. Score 0.581 Taking the results from Round 5 Chains 31, Residues 247, Estimated correctness of the model 0.0 % 2 chains (38 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6183 restraints for refining 3020 atoms. 5073 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2601 (Rfree = 0.000) for 3020 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 12: After refmac, R = 0.2620 (Rfree = 0.000) for 2985 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 13: After refmac, R = 0.2590 (Rfree = 0.000) for 2972 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 14: After refmac, R = 0.2407 (Rfree = 0.000) for 2965 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 15: After refmac, R = 0.2471 (Rfree = 0.000) for 2952 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.80 3.09 Search for helices and strands: 0 residues in 0 chains, 3078 seeds are put forward NCS extension: 41 residues added (5 deleted due to clashes), 3119 seeds are put forward Round 1: 219 peptides, 31 chains. Longest chain 17 peptides. Score 0.443 Round 2: 232 peptides, 30 chains. Longest chain 16 peptides. Score 0.485 Round 3: 243 peptides, 31 chains. Longest chain 19 peptides. Score 0.499 Round 4: 248 peptides, 30 chains. Longest chain 19 peptides. Score 0.521 Round 5: 245 peptides, 28 chains. Longest chain 29 peptides. Score 0.534 Taking the results from Round 5 Chains 28, Residues 217, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6898 restraints for refining 3020 atoms. 6058 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2737 (Rfree = 0.000) for 3020 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 17: After refmac, R = 0.2599 (Rfree = 0.000) for 2985 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 18: After refmac, R = 0.2637 (Rfree = 0.000) for 2972 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 19: After refmac, R = 0.2192 (Rfree = 0.000) for 2968 atoms. Found 4 (14 requested) and removed 11 (7 requested) atoms. Cycle 20: After refmac, R = 0.2467 (Rfree = 0.000) for 2957 atoms. Found 12 (14 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.86 3.14 Search for helices and strands: 0 residues in 0 chains, 3074 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 3104 seeds are put forward Round 1: 221 peptides, 35 chains. Longest chain 21 peptides. Score 0.403 Round 2: 228 peptides, 28 chains. Longest chain 24 peptides. Score 0.497 Round 3: 218 peptides, 29 chains. Longest chain 14 peptides. Score 0.463 Round 4: 224 peptides, 28 chains. Longest chain 35 peptides. Score 0.488 Round 5: 228 peptides, 29 chains. Longest chain 18 peptides. Score 0.486 Taking the results from Round 2 Chains 28, Residues 200, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6817 restraints for refining 3019 atoms. 6026 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2447 (Rfree = 0.000) for 3019 atoms. Found 10 (14 requested) and removed 13 (7 requested) atoms. Cycle 22: After refmac, R = 0.2313 (Rfree = 0.000) for 2981 atoms. Found 14 (14 requested) and removed 8 (7 requested) atoms. Cycle 23: After refmac, R = 0.2367 (Rfree = 0.000) for 2973 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 24: After refmac, R = 0.2179 (Rfree = 0.000) for 2963 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 25: After refmac, R = 0.2164 (Rfree = 0.000) for 2957 atoms. Found 12 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.77 3.07 Search for helices and strands: 0 residues in 0 chains, 3087 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 3112 seeds are put forward Round 1: 192 peptides, 32 chains. Longest chain 13 peptides. Score 0.362 Round 2: 223 peptides, 31 chains. Longest chain 17 peptides. Score 0.453 Round 3: 232 peptides, 32 chains. Longest chain 16 peptides. Score 0.463 Round 4: 219 peptides, 28 chains. Longest chain 22 peptides. Score 0.476 Round 5: 223 peptides, 28 chains. Longest chain 16 peptides. Score 0.485 Taking the results from Round 5 Chains 28, Residues 195, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6947 restraints for refining 3019 atoms. 6168 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2551 (Rfree = 0.000) for 3019 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 27: After refmac, R = 0.2433 (Rfree = 0.000) for 3000 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 28: After refmac, R = 0.2325 (Rfree = 0.000) for 2982 atoms. Found 14 (14 requested) and removed 8 (7 requested) atoms. Cycle 29: After refmac, R = 0.2315 (Rfree = 0.000) for 2972 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 30: After refmac, R = 0.2155 (Rfree = 0.000) for 2961 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.83 3.12 Search for helices and strands: 0 residues in 0 chains, 3084 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3103 seeds are put forward Round 1: 192 peptides, 35 chains. Longest chain 13 peptides. Score 0.326 Round 2: 235 peptides, 34 chains. Longest chain 14 peptides. Score 0.449 Round 3: 223 peptides, 30 chains. Longest chain 17 peptides. Score 0.464 Round 4: 216 peptides, 30 chains. Longest chain 14 peptides. Score 0.447 Round 5: 227 peptides, 31 chains. Longest chain 24 peptides. Score 0.462 Taking the results from Round 3 Chains 30, Residues 193, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6775 restraints for refining 3018 atoms. 5966 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2712 (Rfree = 0.000) for 3018 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 32: After refmac, R = 0.2643 (Rfree = 0.000) for 2986 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 33: After refmac, R = 0.2681 (Rfree = 0.000) for 2964 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 34: After refmac, R = 0.2596 (Rfree = 0.000) for 2943 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 35: After refmac, R = 0.2568 (Rfree = 0.000) for 2917 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.78 3.08 Search for helices and strands: 0 residues in 0 chains, 3056 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 3073 seeds are put forward Round 1: 188 peptides, 35 chains. Longest chain 12 peptides. Score 0.315 Round 2: 214 peptides, 31 chains. Longest chain 16 peptides. Score 0.431 Round 3: 212 peptides, 29 chains. Longest chain 23 peptides. Score 0.448 Round 4: 225 peptides, 32 chains. Longest chain 16 peptides. Score 0.447 Round 5: 222 peptides, 31 chains. Longest chain 13 peptides. Score 0.450 Taking the results from Round 5 Chains 31, Residues 191, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6978 restraints for refining 3020 atoms. 6245 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2635 (Rfree = 0.000) for 3020 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 37: After refmac, R = 0.2635 (Rfree = 0.000) for 2991 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 38: After refmac, R = 0.2122 (Rfree = 0.000) for 2971 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 39: After refmac, R = 0.2318 (Rfree = 0.000) for 2967 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 40: After refmac, R = 0.2618 (Rfree = 0.000) for 2961 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.76 3.06 Search for helices and strands: 0 residues in 0 chains, 3093 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3106 seeds are put forward Round 1: 188 peptides, 34 chains. Longest chain 11 peptides. Score 0.327 Round 2: 210 peptides, 33 chains. Longest chain 11 peptides. Score 0.398 Round 3: 222 peptides, 34 chains. Longest chain 12 peptides. Score 0.417 Round 4: 223 peptides, 29 chains. Longest chain 28 peptides. Score 0.474 Round 5: 211 peptides, 30 chains. Longest chain 20 peptides. Score 0.434 Taking the results from Round 4 Chains 30, Residues 194, Estimated correctness of the model 0.0 % 2 chains (33 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6492 restraints for refining 3019 atoms. 5614 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2600 (Rfree = 0.000) for 3019 atoms. Found 14 (14 requested) and removed 43 (7 requested) atoms. Cycle 42: After refmac, R = 0.2595 (Rfree = 0.000) for 2979 atoms. Found 14 (14 requested) and removed 42 (7 requested) atoms. Cycle 43: After refmac, R = 0.2448 (Rfree = 0.000) for 2939 atoms. Found 14 (14 requested) and removed 29 (7 requested) atoms. Cycle 44: After refmac, R = 0.2433 (Rfree = 0.000) for 2913 atoms. Found 13 (13 requested) and removed 28 (6 requested) atoms. Cycle 45: After refmac, R = 0.2522 (Rfree = 0.000) for 2884 atoms. Found 13 (13 requested) and removed 26 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.74 3.04 Search for helices and strands: 0 residues in 0 chains, 3005 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 3030 seeds are put forward Round 1: 183 peptides, 33 chains. Longest chain 11 peptides. Score 0.325 Round 2: 215 peptides, 34 chains. Longest chain 13 peptides. Score 0.399 Round 3: 209 peptides, 33 chains. Longest chain 11 peptides. Score 0.395 Round 4: 212 peptides, 33 chains. Longest chain 12 peptides. Score 0.403 Round 5: 217 peptides, 34 chains. Longest chain 19 peptides. Score 0.404 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 183, 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 2p8j-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5718 reflections ( 98.03 % complete ) and 6991 restraints for refining 3020 atoms. 6293 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2722 (Rfree = 0.000) for 3020 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2516 (Rfree = 0.000) for 3001 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2445 (Rfree = 0.000) for 2988 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2432 (Rfree = 0.000) for 2971 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:28:02 GMT 2018 Job finished. TimeTaking 60.12 Used memory is bytes: 16863784