null Sun 23 Dec 22:22:46 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 1vjr-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjr-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjr-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjr-3.8-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/1vjr-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjr-3.8-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 ============================================================ Sun 23 Dec 22:22:56 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/1vjr-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjr-3.8-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 450 and 0 Target number of residues in the AU: 450 Target solvent content: 0.6562 Checking the provided sequence file Detected sequence length: 271 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 542 Adjusted target solvent content: 0.59 Input MTZ file: 1vjr-3.8-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: 92 Cell parameters: 93.998 93.998 160.365 90.000 90.000 90.000 Input sequence file: 1vjr-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 4336 target number of atoms Had to go as low as 0.65 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: 81.094 3.800 Wilson plot Bfac: 81.82 7550 reflections ( 99.91 % complete ) and 0 restraints for refining 4797 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3510 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3416 (Rfree = 0.000) for 4797 atoms. Found 26 (26 requested) and removed 138 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.63 3.22 Search for helices and strands: 0 residues in 0 chains, 4702 seeds are put forward NCS extension: 0 residues added, 4702 seeds are put forward Round 1: 177 peptides, 23 chains. Longest chain 27 peptides. Score 0.415 Round 2: 197 peptides, 17 chains. Longest chain 36 peptides. Score 0.524 Round 3: 190 peptides, 23 chains. Longest chain 19 peptides. Score 0.445 Round 4: 192 peptides, 15 chains. Longest chain 26 peptides. Score 0.535 Round 5: 193 peptides, 18 chains. Longest chain 25 peptides. Score 0.506 Taking the results from Round 4 Chains 15, Residues 177, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7550 reflections ( 99.91 % complete ) and 8383 restraints for refining 3584 atoms. 7690 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2753 (Rfree = 0.000) for 3584 atoms. Found 19 (19 requested) and removed 56 (9 requested) atoms. Cycle 2: After refmac, R = 0.2591 (Rfree = 0.000) for 3444 atoms. Found 19 (19 requested) and removed 54 (9 requested) atoms. Cycle 3: After refmac, R = 0.2611 (Rfree = 0.000) for 3372 atoms. Found 18 (18 requested) and removed 36 (9 requested) atoms. Cycle 4: After refmac, R = 0.2636 (Rfree = 0.000) for 3310 atoms. Found 18 (18 requested) and removed 36 (9 requested) atoms. Cycle 5: After refmac, R = 0.2533 (Rfree = 0.000) for 3253 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 3.25 Search for helices and strands: 0 residues in 0 chains, 3331 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 3359 seeds are put forward Round 1: 175 peptides, 26 chains. Longest chain 13 peptides. Score 0.376 Round 2: 211 peptides, 25 chains. Longest chain 23 peptides. Score 0.471 Round 3: 220 peptides, 21 chains. Longest chain 30 peptides. Score 0.530 Round 4: 211 peptides, 23 chains. Longest chain 22 peptides. Score 0.491 Round 5: 200 peptides, 21 chains. Longest chain 26 peptides. Score 0.489 Taking the results from Round 3 Chains 24, Residues 199, Estimated correctness of the model 0.0 % 3 chains (47 residues) have been docked in sequence ------------------------------------------------------ 7550 reflections ( 99.91 % complete ) and 6220 restraints for refining 3197 atoms. 5290 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2529 (Rfree = 0.000) for 3197 atoms. Found 17 (17 requested) and removed 47 (8 requested) atoms. Cycle 7: After refmac, R = 0.2633 (Rfree = 0.000) for 3094 atoms. Found 17 (17 requested) and removed 44 (8 requested) atoms. Cycle 8: After refmac, R = 0.2457 (Rfree = 0.000) for 3030 atoms. Found 16 (16 requested) and removed 29 (8 requested) atoms. Cycle 9: After refmac, R = 0.2413 (Rfree = 0.000) for 2982 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 10: After refmac, R = 0.2424 (Rfree = 0.000) for 2947 atoms. Found 16 (16 requested) and removed 42 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.52 3.12 Search for helices and strands: 0 residues in 0 chains, 2994 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3012 seeds are put forward Round 1: 213 peptides, 27 chains. Longest chain 26 peptides. Score 0.454 Round 2: 212 peptides, 23 chains. Longest chain 28 peptides. Score 0.494 Round 3: 210 peptides, 21 chains. Longest chain 38 peptides. Score 0.510 Round 4: 237 peptides, 29 chains. Longest chain 21 peptides. Score 0.486 Round 5: 218 peptides, 20 chains. Longest chain 23 peptides. Score 0.536 Taking the results from Round 5 Chains 22, Residues 198, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 7550 reflections ( 99.91 % complete ) and 6492 restraints for refining 3203 atoms. 5631 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2617 (Rfree = 0.000) for 3203 atoms. Found 17 (17 requested) and removed 41 (8 requested) atoms. Cycle 12: After refmac, R = 0.2360 (Rfree = 0.000) for 3128 atoms. Found 17 (17 requested) and removed 30 (8 requested) atoms. Cycle 13: After refmac, R = 0.2372 (Rfree = 0.000) for 3094 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 14: After refmac, R = 0.2314 (Rfree = 0.000) for 3068 atoms. Found 15 (16 requested) and removed 17 (8 requested) atoms. Cycle 15: After refmac, R = 0.2349 (Rfree = 0.000) for 3045 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.61 3.20 Search for helices and strands: 0 residues in 0 chains, 3116 seeds are put forward NCS extension: 37 residues added (5 deleted due to clashes), 3153 seeds are put forward Round 1: 201 peptides, 25 chains. Longest chain 22 peptides. Score 0.449 Round 2: 216 peptides, 26 chains. Longest chain 17 peptides. Score 0.471 Round 3: 213 peptides, 27 chains. Longest chain 25 peptides. Score 0.454 Round 4: 218 peptides, 30 chains. Longest chain 16 peptides. Score 0.434 Round 5: 215 peptides, 23 chains. Longest chain 20 peptides. Score 0.500 Taking the results from Round 5 Chains 23, Residues 192, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7550 reflections ( 99.91 % complete ) and 7172 restraints for refining 3231 atoms. 6427 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2592 (Rfree = 0.000) for 3231 atoms. Found 17 (17 requested) and removed 96 (8 requested) atoms. Cycle 17: After refmac, R = 0.2490 (Rfree = 0.000) for 3106 atoms. Found 17 (17 requested) and removed 47 (8 requested) atoms. Cycle 18: After refmac, R = 0.2349 (Rfree = 0.000) for 3042 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 19: After refmac, R = 0.2305 (Rfree = 0.000) for 3011 atoms. Found 16 (16 requested) and removed 39 (8 requested) atoms. Cycle 20: After refmac, R = 0.2318 (Rfree = 0.000) for 2976 atoms. Found 16 (16 requested) and removed 26 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.60 3.19 Search for helices and strands: 0 residues in 0 chains, 3097 seeds are put forward NCS extension: 11 residues added (4 deleted due to clashes), 3108 seeds are put forward Round 1: 191 peptides, 29 chains. Longest chain 14 peptides. Score 0.381 Round 2: 208 peptides, 20 chains. Longest chain 20 peptides. Score 0.516 Round 3: 214 peptides, 21 chains. Longest chain 31 peptides. Score 0.518 Round 4: 213 peptides, 24 chains. Longest chain 24 peptides. Score 0.485 Round 5: 201 peptides, 20 chains. Longest chain 24 peptides. Score 0.501 Taking the results from Round 3 Chains 23, Residues 193, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 7550 reflections ( 99.91 % complete ) and 6087 restraints for refining 3041 atoms. 5235 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2381 (Rfree = 0.000) for 3041 atoms. Found 16 (16 requested) and removed 33 (8 requested) atoms. Cycle 22: After refmac, R = 0.2300 (Rfree = 0.000) for 2995 atoms. Found 16 (16 requested) and removed 32 (8 requested) atoms. Cycle 23: After refmac, R = 0.2238 (Rfree = 0.000) for 2961 atoms. Found 16 (16 requested) and removed 29 (8 requested) atoms. Cycle 24: After refmac, R = 0.2191 (Rfree = 0.000) for 2932 atoms. Found 15 (16 requested) and removed 21 (8 requested) atoms. Cycle 25: After refmac, R = 0.2112 (Rfree = 0.000) for 2913 atoms. Found 16 (16 requested) and removed 26 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.63 3.22 Search for helices and strands: 0 residues in 0 chains, 2962 seeds are put forward NCS extension: 34 residues added (0 deleted due to clashes), 2996 seeds are put forward Round 1: 203 peptides, 29 chains. Longest chain 20 peptides. Score 0.410 Round 2: 209 peptides, 24 chains. Longest chain 35 peptides. Score 0.477 Round 3: 193 peptides, 23 chains. Longest chain 29 peptides. Score 0.452 Round 4: 204 peptides, 21 chains. Longest chain 26 peptides. Score 0.497 Round 5: 193 peptides, 21 chains. Longest chain 23 peptides. Score 0.474 Taking the results from Round 4 Chains 21, Residues 183, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7550 reflections ( 99.91 % complete ) and 6641 restraints for refining 3091 atoms. 5930 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2395 (Rfree = 0.000) for 3091 atoms. Found 16 (16 requested) and removed 32 (8 requested) atoms. Cycle 27: After refmac, R = 0.2210 (Rfree = 0.000) for 3049 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 28: After refmac, R = 0.2206 (Rfree = 0.000) for 3034 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 29: After refmac, R = 0.2270 (Rfree = 0.000) for 3022 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 30: After refmac, R = 0.2127 (Rfree = 0.000) for 3007 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 3.18 Search for helices and strands: 0 residues in 0 chains, 3095 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 3120 seeds are put forward Round 1: 192 peptides, 26 chains. Longest chain 17 peptides. Score 0.417 Round 2: 197 peptides, 24 chains. Longest chain 19 peptides. Score 0.450 Round 3: 202 peptides, 23 chains. Longest chain 18 peptides. Score 0.472 Round 4: 181 peptides, 19 chains. Longest chain 19 peptides. Score 0.469 Round 5: 199 peptides, 23 chains. Longest chain 28 peptides. Score 0.465 Taking the results from Round 3 Chains 25, Residues 179, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 7550 reflections ( 99.91 % complete ) and 6620 restraints for refining 3107 atoms. 5893 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2289 (Rfree = 0.000) for 3107 atoms. Found 17 (17 requested) and removed 28 (8 requested) atoms. Cycle 32: After refmac, R = 0.2298 (Rfree = 0.000) for 3074 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 33: After refmac, R = 0.2204 (Rfree = 0.000) for 3061 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 34: After refmac, R = 0.2238 (Rfree = 0.000) for 3050 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 35: After refmac, R = 0.2154 (Rfree = 0.000) for 3042 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.61 3.20 Search for helices and strands: 0 residues in 0 chains, 3131 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3153 seeds are put forward Round 1: 181 peptides, 26 chains. Longest chain 14 peptides. Score 0.391 Round 2: 216 peptides, 26 chains. Longest chain 20 peptides. Score 0.471 Round 3: 217 peptides, 27 chains. Longest chain 26 peptides. Score 0.463 Round 4: 213 peptides, 26 chains. Longest chain 27 peptides. Score 0.465 Round 5: 219 peptides, 25 chains. Longest chain 31 peptides. Score 0.488 Taking the results from Round 5 Chains 25, Residues 194, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7550 reflections ( 99.91 % complete ) and 6697 restraints for refining 3121 atoms. 5946 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2524 (Rfree = 0.000) for 3121 atoms. Found 17 (17 requested) and removed 44 (8 requested) atoms. Cycle 37: After refmac, R = 0.2405 (Rfree = 0.000) for 3070 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 38: After refmac, R = 0.2351 (Rfree = 0.000) for 3055 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 39: After refmac, R = 0.2266 (Rfree = 0.000) for 3051 atoms. Found 16 (16 requested) and removed 29 (8 requested) atoms. Cycle 40: After refmac, R = 0.2232 (Rfree = 0.000) for 3030 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.25 Search for helices and strands: 0 residues in 0 chains, 3139 seeds are put forward NCS extension: 35 residues added (2 deleted due to clashes), 3174 seeds are put forward Round 1: 170 peptides, 23 chains. Longest chain 16 peptides. Score 0.398 Round 2: 185 peptides, 23 chains. Longest chain 17 peptides. Score 0.434 Round 3: 202 peptides, 24 chains. Longest chain 22 peptides. Score 0.461 Round 4: 192 peptides, 24 chains. Longest chain 18 peptides. Score 0.439 Round 5: 201 peptides, 24 chains. Longest chain 15 peptides. Score 0.459 Taking the results from Round 3 Chains 24, Residues 178, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7550 reflections ( 99.91 % complete ) and 6565 restraints for refining 3052 atoms. 5877 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2453 (Rfree = 0.000) for 3052 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. Cycle 42: After refmac, R = 0.2226 (Rfree = 0.000) for 3025 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. Cycle 43: After refmac, R = 0.2195 (Rfree = 0.000) for 3012 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 44: After refmac, R = 0.2161 (Rfree = 0.000) for 2996 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 45: After refmac, R = 0.2187 (Rfree = 0.000) for 2985 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 3.24 Search for helices and strands: 0 residues in 0 chains, 3086 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 3112 seeds are put forward Round 1: 183 peptides, 24 chains. Longest chain 21 peptides. Score 0.418 Round 2: 213 peptides, 28 chains. Longest chain 22 peptides. Score 0.444 Round 3: 194 peptides, 24 chains. Longest chain 14 peptides. Score 0.444 Round 4: 195 peptides, 20 chains. Longest chain 26 peptides. Score 0.489 Round 5: 200 peptides, 24 chains. Longest chain 30 peptides. Score 0.457 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 175, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1vjr-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7550 reflections ( 99.91 % complete ) and 6540 restraints for refining 3046 atoms. 5834 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2350 (Rfree = 0.000) for 3046 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2381 (Rfree = 0.000) for 3006 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2431 (Rfree = 0.000) for 2991 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2443 (Rfree = 0.000) for 2973 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:22:31 GMT 2018 Job finished. TimeTaking 59.75 Used memory is bytes: 19163728