Sun 23 Dec 22:23:05 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 2a6a-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a6a-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a6a-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6a-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/2a6a-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6a-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 ============================================================ Sun 23 Dec 22:23:13 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/2a6a-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6a-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 330 and 0 Target number of residues in the AU: 330 Target solvent content: 0.6609 Checking the provided sequence file Detected sequence length: 218 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 436 Adjusted target solvent content: 0.55 Input MTZ file: 2a6a-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: 21 Cell parameters: 93.313 217.176 51.977 90.000 90.000 90.000 Input sequence file: 2a6a-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 3488 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: 108.588 3.400 Wilson plot Bfac: 85.40 7577 reflections ( 98.98 % complete ) and 0 restraints for refining 3846 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3463 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3378 (Rfree = 0.000) for 3846 atoms. Found 29 (29 requested) and removed 62 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.50 3.27 Search for helices and strands: 0 residues in 0 chains, 3897 seeds are put forward NCS extension: 0 residues added, 3897 seeds are put forward Round 1: 183 peptides, 32 chains. Longest chain 12 peptides. Score 0.364 Round 2: 208 peptides, 29 chains. Longest chain 19 peptides. Score 0.480 Round 3: 225 peptides, 33 chains. Longest chain 17 peptides. Score 0.477 Round 4: 226 peptides, 31 chains. Longest chain 18 peptides. Score 0.504 Round 5: 244 peptides, 33 chains. Longest chain 19 peptides. Score 0.528 Taking the results from Round 5 Chains 34, Residues 211, Estimated correctness of the model 3.4 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 7577 reflections ( 98.98 % complete ) and 7212 restraints for refining 3170 atoms. 6339 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2822 (Rfree = 0.000) for 3170 atoms. Found 15 (23 requested) and removed 26 (11 requested) atoms. Cycle 2: After refmac, R = 0.2684 (Rfree = 0.000) for 3097 atoms. Found 20 (23 requested) and removed 21 (11 requested) atoms. Cycle 3: After refmac, R = 0.2673 (Rfree = 0.000) for 3066 atoms. Found 10 (23 requested) and removed 18 (11 requested) atoms. Cycle 4: After refmac, R = 0.2349 (Rfree = 0.000) for 3036 atoms. Found 12 (23 requested) and removed 14 (11 requested) atoms. Cycle 5: After refmac, R = 0.2480 (Rfree = 0.000) for 3024 atoms. Found 18 (22 requested) and removed 25 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.52 3.29 Search for helices and strands: 0 residues in 0 chains, 3117 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 3141 seeds are put forward Round 1: 216 peptides, 31 chains. Longest chain 16 peptides. Score 0.477 Round 2: 257 peptides, 32 chains. Longest chain 22 peptides. Score 0.572 Round 3: 250 peptides, 30 chains. Longest chain 20 peptides. Score 0.577 Round 4: 245 peptides, 26 chains. Longest chain 20 peptides. Score 0.609 Round 5: 255 peptides, 33 chains. Longest chain 18 peptides. Score 0.556 Taking the results from Round 4 Chains 28, Residues 219, Estimated correctness of the model 31.6 % 3 chains (47 residues) have been docked in sequence ------------------------------------------------------ 7577 reflections ( 98.98 % complete ) and 6497 restraints for refining 3171 atoms. 5448 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2525 (Rfree = 0.000) for 3171 atoms. Found 23 (23 requested) and removed 25 (11 requested) atoms. Cycle 7: After refmac, R = 0.2328 (Rfree = 0.000) for 3142 atoms. Found 11 (23 requested) and removed 22 (11 requested) atoms. Cycle 8: After refmac, R = 0.2588 (Rfree = 0.000) for 3094 atoms. Found 22 (23 requested) and removed 25 (11 requested) atoms. Cycle 9: After refmac, R = 0.2951 (Rfree = 0.000) for 3071 atoms. Found 23 (23 requested) and removed 38 (11 requested) atoms. Cycle 10: After refmac, R = 0.2799 (Rfree = 0.000) for 3031 atoms. Found 23 (23 requested) and removed 31 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.52 3.29 Search for helices and strands: 0 residues in 0 chains, 3145 seeds are put forward NCS extension: 22 residues added (6 deleted due to clashes), 3167 seeds are put forward Round 1: 242 peptides, 36 chains. Longest chain 16 peptides. Score 0.487 Round 2: 265 peptides, 30 chains. Longest chain 29 peptides. Score 0.612 Round 3: 250 peptides, 28 chains. Longest chain 22 peptides. Score 0.599 Round 4: 274 peptides, 32 chains. Longest chain 23 peptides. Score 0.612 Round 5: 271 peptides, 35 chains. Longest chain 19 peptides. Score 0.573 Taking the results from Round 4 Chains 32, Residues 242, Estimated correctness of the model 32.5 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ 7577 reflections ( 98.98 % complete ) and 6540 restraints for refining 3171 atoms. 5473 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2660 (Rfree = 0.000) for 3171 atoms. Found 23 (23 requested) and removed 38 (11 requested) atoms. Cycle 12: After refmac, R = 0.2500 (Rfree = 0.000) for 3117 atoms. Found 23 (23 requested) and removed 23 (11 requested) atoms. Cycle 13: After refmac, R = 0.2302 (Rfree = 0.000) for 3098 atoms. Found 15 (23 requested) and removed 26 (11 requested) atoms. Cycle 14: After refmac, R = 0.2307 (Rfree = 0.000) for 3069 atoms. Found 21 (23 requested) and removed 27 (11 requested) atoms. Cycle 15: After refmac, R = 0.2297 (Rfree = 0.000) for 3052 atoms. Found 20 (23 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 3.26 Search for helices and strands: 0 residues in 0 chains, 3167 seeds are put forward NCS extension: 33 residues added (4 deleted due to clashes), 3200 seeds are put forward Round 1: 234 peptides, 35 chains. Longest chain 22 peptides. Score 0.478 Round 2: 239 peptides, 29 chains. Longest chain 24 peptides. Score 0.562 Round 3: 245 peptides, 30 chains. Longest chain 20 peptides. Score 0.565 Round 4: 250 peptides, 29 chains. Longest chain 17 peptides. Score 0.588 Round 5: 269 peptides, 24 chains. Longest chain 32 peptides. Score 0.679 Taking the results from Round 5 Chains 26, Residues 245, Estimated correctness of the model 52.3 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7577 reflections ( 98.98 % complete ) and 6767 restraints for refining 3171 atoms. 5780 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2634 (Rfree = 0.000) for 3171 atoms. Found 23 (23 requested) and removed 31 (11 requested) atoms. Cycle 17: After refmac, R = 0.2285 (Rfree = 0.000) for 3131 atoms. Found 21 (23 requested) and removed 32 (11 requested) atoms. Cycle 18: After refmac, R = 0.2257 (Rfree = 0.000) for 3105 atoms. Found 21 (23 requested) and removed 18 (11 requested) atoms. Cycle 19: After refmac, R = 0.2086 (Rfree = 0.000) for 3093 atoms. Found 10 (23 requested) and removed 16 (11 requested) atoms. Cycle 20: After refmac, R = 0.2552 (Rfree = 0.000) for 3072 atoms. Found 23 (23 requested) and removed 21 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 3.28 Search for helices and strands: 0 residues in 0 chains, 3183 seeds are put forward NCS extension: 59 residues added (3 deleted due to clashes), 3242 seeds are put forward Round 1: 233 peptides, 32 chains. Longest chain 23 peptides. Score 0.511 Round 2: 257 peptides, 28 chains. Longest chain 26 peptides. Score 0.615 Round 3: 266 peptides, 26 chains. Longest chain 35 peptides. Score 0.654 Round 4: 262 peptides, 31 chains. Longest chain 23 peptides. Score 0.595 Round 5: 265 peptides, 29 chains. Longest chain 38 peptides. Score 0.622 Taking the results from Round 3 Chains 27, Residues 240, Estimated correctness of the model 45.3 % 2 chains (49 residues) have been docked in sequence ------------------------------------------------------ 7577 reflections ( 98.98 % complete ) and 6359 restraints for refining 3171 atoms. 5215 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2368 (Rfree = 0.000) for 3171 atoms. Found 16 (23 requested) and removed 42 (11 requested) atoms. Cycle 22: After refmac, R = 0.2532 (Rfree = 0.000) for 3133 atoms. Found 23 (23 requested) and removed 32 (11 requested) atoms. Cycle 23: After refmac, R = 0.2678 (Rfree = 0.000) for 3111 atoms. Found 23 (23 requested) and removed 62 (11 requested) atoms. Cycle 24: After refmac, R = 0.2495 (Rfree = 0.000) for 3063 atoms. Found 23 (23 requested) and removed 24 (11 requested) atoms. Cycle 25: After refmac, R = 0.2586 (Rfree = 0.000) for 3054 atoms. Found 23 (23 requested) and removed 28 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.50 3.27 Search for helices and strands: 0 residues in 0 chains, 3145 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3162 seeds are put forward Round 1: 241 peptides, 28 chains. Longest chain 19 peptides. Score 0.578 Round 2: 269 peptides, 32 chains. Longest chain 19 peptides. Score 0.600 Round 3: 277 peptides, 29 chains. Longest chain 25 peptides. Score 0.648 Round 4: 261 peptides, 27 chains. Longest chain 20 peptides. Score 0.634 Round 5: 257 peptides, 25 chains. Longest chain 22 peptides. Score 0.645 Taking the results from Round 3 Chains 29, Residues 248, Estimated correctness of the model 43.6 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 7577 reflections ( 98.98 % complete ) and 6617 restraints for refining 3171 atoms. 5600 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2316 (Rfree = 0.000) for 3171 atoms. Found 17 (23 requested) and removed 43 (11 requested) atoms. Cycle 27: After refmac, R = 0.2536 (Rfree = 0.000) for 3135 atoms. Found 23 (23 requested) and removed 26 (11 requested) atoms. Cycle 28: After refmac, R = 0.2651 (Rfree = 0.000) for 3118 atoms. Found 23 (23 requested) and removed 25 (11 requested) atoms. Cycle 29: After refmac, R = 0.2883 (Rfree = 0.000) for 3097 atoms. Found 23 (23 requested) and removed 27 (11 requested) atoms. Cycle 30: After refmac, R = 0.1922 (Rfree = 0.000) for 3076 atoms. Found 13 (23 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.51 3.28 Search for helices and strands: 0 residues in 0 chains, 3202 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 3229 seeds are put forward Round 1: 238 peptides, 31 chains. Longest chain 29 peptides. Score 0.536 Round 2: 272 peptides, 30 chains. Longest chain 30 peptides. Score 0.627 Round 3: 276 peptides, 30 chains. Longest chain 30 peptides. Score 0.636 Round 4: 284 peptides, 29 chains. Longest chain 38 peptides. Score 0.662 Round 5: 259 peptides, 27 chains. Longest chain 20 peptides. Score 0.630 Taking the results from Round 4 Chains 30, Residues 255, Estimated correctness of the model 47.6 % 4 chains (69 residues) have been docked in sequence ------------------------------------------------------ 7577 reflections ( 98.98 % complete ) and 5942 restraints for refining 3171 atoms. 4650 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2619 (Rfree = 0.000) for 3171 atoms. Found 16 (23 requested) and removed 85 (11 requested) atoms. Cycle 32: After refmac, R = 0.2573 (Rfree = 0.000) for 3075 atoms. Found 23 (23 requested) and removed 48 (11 requested) atoms. Cycle 33: After refmac, R = 0.2125 (Rfree = 0.000) for 3036 atoms. Found 10 (23 requested) and removed 15 (11 requested) atoms. Cycle 34: After refmac, R = 0.2464 (Rfree = 0.000) for 3025 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 35: After refmac, R = 0.2042 (Rfree = 0.000) for 3017 atoms. Found 12 (22 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.52 3.29 Search for helices and strands: 0 residues in 0 chains, 3088 seeds are put forward NCS extension: 92 residues added (10 deleted due to clashes), 3180 seeds are put forward Round 1: 227 peptides, 32 chains. Longest chain 19 peptides. Score 0.495 Round 2: 245 peptides, 27 chains. Longest chain 43 peptides. Score 0.598 Round 3: 237 peptides, 27 chains. Longest chain 23 peptides. Score 0.579 Round 4: 248 peptides, 24 chains. Longest chain 40 peptides. Score 0.636 Round 5: 246 peptides, 28 chains. Longest chain 35 peptides. Score 0.590 Taking the results from Round 4 Chains 27, Residues 224, Estimated correctness of the model 40.0 % 4 chains (50 residues) have been docked in sequence ------------------------------------------------------ 7577 reflections ( 98.98 % complete ) and 6156 restraints for refining 3117 atoms. 5099 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2535 (Rfree = 0.000) for 3117 atoms. Found 22 (23 requested) and removed 39 (11 requested) atoms. Cycle 37: After refmac, R = 0.2227 (Rfree = 0.000) for 3081 atoms. Found 16 (23 requested) and removed 18 (11 requested) atoms. Cycle 38: After refmac, R = 0.2059 (Rfree = 0.000) for 3061 atoms. Found 20 (23 requested) and removed 14 (11 requested) atoms. Cycle 39: After refmac, R = 0.2309 (Rfree = 0.000) for 3056 atoms. Found 23 (23 requested) and removed 17 (11 requested) atoms. Cycle 40: After refmac, R = 0.2059 (Rfree = 0.000) for 3055 atoms. Found 18 (23 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.29 Search for helices and strands: 0 residues in 0 chains, 3145 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 3170 seeds are put forward Round 1: 207 peptides, 31 chains. Longest chain 20 peptides. Score 0.451 Round 2: 223 peptides, 25 chains. Longest chain 34 peptides. Score 0.568 Round 3: 225 peptides, 25 chains. Longest chain 20 peptides. Score 0.573 Round 4: 225 peptides, 26 chains. Longest chain 20 peptides. Score 0.561 Round 5: 224 peptides, 28 chains. Longest chain 20 peptides. Score 0.535 Taking the results from Round 3 Chains 25, Residues 200, Estimated correctness of the model 19.6 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 7577 reflections ( 98.98 % complete ) and 6432 restraints for refining 3097 atoms. 5578 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2468 (Rfree = 0.000) for 3097 atoms. Found 23 (23 requested) and removed 40 (11 requested) atoms. Cycle 42: After refmac, R = 0.2219 (Rfree = 0.000) for 3074 atoms. Found 21 (23 requested) and removed 25 (11 requested) atoms. Cycle 43: After refmac, R = 0.2510 (Rfree = 0.000) for 3063 atoms. Found 23 (23 requested) and removed 37 (11 requested) atoms. Cycle 44: After refmac, R = 0.2163 (Rfree = 0.000) for 3042 atoms. Found 18 (22 requested) and removed 18 (11 requested) atoms. Cycle 45: After refmac, R = 0.2618 (Rfree = 0.000) for 3028 atoms. Found 22 (22 requested) and removed 33 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.49 3.26 Search for helices and strands: 0 residues in 0 chains, 3128 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 3154 seeds are put forward Round 1: 203 peptides, 29 chains. Longest chain 20 peptides. Score 0.465 Round 2: 225 peptides, 29 chains. Longest chain 20 peptides. Score 0.526 Round 3: 223 peptides, 27 chains. Longest chain 20 peptides. Score 0.544 Round 4: 237 peptides, 30 chains. Longest chain 20 peptides. Score 0.545 Round 5: 230 peptides, 32 chains. Longest chain 17 peptides. Score 0.503 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 207, Estimated correctness of the model 9.7 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2a6a-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7577 reflections ( 98.98 % complete ) and 6443 restraints for refining 3070 atoms. 5645 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2782 (Rfree = 0.000) for 3070 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2297 (Rfree = 0.000) for 3044 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1988 (Rfree = 0.000) for 3026 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2077 (Rfree = 0.000) for 3008 atoms. TimeTaking 59.57