Sun 23 Dec 22:23:10 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 1vra-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vra-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vra-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vra-3.2-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/1vra-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vra-3.2-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 22:23:18 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/1vra-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vra-3.2-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 432 and 0 Target number of residues in the AU: 432 Target solvent content: 0.5787 Checking the provided sequence file Detected sequence length: 423 Maximum limit of NCS related copies: 30 Number of NCS-related molecules: 1 Adjusted target number of residues: 423 Adjusted target solvent content: 0.59 Input MTZ file: 1vra-3.2-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: 70.658 70.658 222.292 90.000 90.000 90.000 Input sequence file: 1vra-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 3384 target number of atoms Had to go as low as 0.80 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 Loops will be built when appropriate and at the last cycle Resolution range: 29.814 3.200 Wilson plot Bfac: 44.33 9938 reflections ( 99.76 % complete ) and 0 restraints for refining 3747 atoms. Observations/parameters ratio is 0.66 ------------------------------------------------------ Starting model: R = 0.3670 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3366 (Rfree = 0.000) for 3747 atoms. Found 33 (33 requested) and removed 58 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.84 2.52 Search for helices and strands: 0 residues in 0 chains, 3810 seeds are put forward Round 1: 264 peptides, 42 chains. Longest chain 13 peptides. Score 0.464 Round 2: 305 peptides, 37 chains. Longest chain 29 peptides. Score 0.615 Round 3: 327 peptides, 31 chains. Longest chain 26 peptides. Score 0.708 Round 4: 326 peptides, 29 chains. Longest chain 29 peptides. Score 0.722 Round 5: 314 peptides, 27 chains. Longest chain 36 peptides. Score 0.718 Taking the results from Round 4 Chains 33, Residues 297, Estimated correctness of the model 69.7 % 5 chains (74 residues) have been docked in sequence Building loops using Loopy2018 33 chains (297 residues) following loop building 5 chains (74 residues) in sequence following loop building ------------------------------------------------------ 9938 reflections ( 99.76 % complete ) and 5537 restraints for refining 3089 atoms. 4125 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3253 (Rfree = 0.000) for 3089 atoms. Found 27 (27 requested) and removed 33 (13 requested) atoms. Cycle 2: After refmac, R = 0.3077 (Rfree = 0.000) for 3039 atoms. Found 22 (26 requested) and removed 18 (13 requested) atoms. Cycle 3: After refmac, R = 0.2998 (Rfree = 0.000) for 3024 atoms. Found 14 (26 requested) and removed 20 (13 requested) atoms. Cycle 4: After refmac, R = 0.2942 (Rfree = 0.000) for 3014 atoms. Found 12 (25 requested) and removed 16 (13 requested) atoms. Cycle 5: After refmac, R = 0.2879 (Rfree = 0.000) for 3007 atoms. Found 15 (25 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.93 2.60 Search for helices and strands: 0 residues in 0 chains, 3138 seeds are put forward Round 1: 298 peptides, 39 chains. Longest chain 19 peptides. Score 0.580 Round 2: 329 peptides, 32 chains. Longest chain 30 peptides. Score 0.703 Round 3: 349 peptides, 24 chains. Longest chain 40 peptides. Score 0.790 Round 4: 345 peptides, 31 chains. Longest chain 40 peptides. Score 0.736 Round 5: 332 peptides, 27 chains. Longest chain 41 peptides. Score 0.746 Taking the results from Round 3 Chains 32, Residues 325, Estimated correctness of the model 81.9 % 9 chains (156 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 A and 48 A Built loop between residues 85 B and 93 B Built loop between residues 105 B and 110 B Built loop between residues 128 B and 132 B 26 chains (333 residues) following loop building 5 chains (177 residues) in sequence following loop building ------------------------------------------------------ 9938 reflections ( 99.76 % complete ) and 4646 restraints for refining 3088 atoms. 2796 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3428 (Rfree = 0.000) for 3088 atoms. Found 24 (24 requested) and removed 43 (13 requested) atoms. Cycle 7: After refmac, R = 0.3175 (Rfree = 0.000) for 3045 atoms. Found 24 (24 requested) and removed 24 (13 requested) atoms. Cycle 8: After refmac, R = 0.3021 (Rfree = 0.000) for 3036 atoms. Found 21 (23 requested) and removed 22 (13 requested) atoms. Cycle 9: After refmac, R = 0.2898 (Rfree = 0.000) for 3030 atoms. Found 17 (23 requested) and removed 21 (13 requested) atoms. Cycle 10: After refmac, R = 0.2785 (Rfree = 0.000) for 3024 atoms. Found 13 (22 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.89 2.56 Search for helices and strands: 0 residues in 0 chains, 3145 seeds are put forward Round 1: 333 peptides, 33 chains. Longest chain 34 peptides. Score 0.702 Round 2: 351 peptides, 26 chains. Longest chain 41 peptides. Score 0.779 Round 3: 340 peptides, 31 chains. Longest chain 37 peptides. Score 0.729 Round 4: 332 peptides, 29 chains. Longest chain 31 peptides. Score 0.731 Round 5: 328 peptides, 26 chains. Longest chain 24 peptides. Score 0.748 Taking the results from Round 2 Chains 32, Residues 325, Estimated correctness of the model 80.1 % 7 chains (113 residues) have been docked in sequence Building loops using Loopy2018 32 chains (325 residues) following loop building 7 chains (113 residues) in sequence following loop building ------------------------------------------------------ 9938 reflections ( 99.76 % complete ) and 5200 restraints for refining 3089 atoms. 3519 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3130 (Rfree = 0.000) for 3089 atoms. Found 22 (22 requested) and removed 36 (13 requested) atoms. Cycle 12: After refmac, R = 0.3094 (Rfree = 0.000) for 3061 atoms. Found 18 (21 requested) and removed 23 (13 requested) atoms. Cycle 13: After refmac, R = 0.2794 (Rfree = 0.000) for 3047 atoms. Found 19 (21 requested) and removed 18 (13 requested) atoms. Cycle 14: After refmac, R = 0.2910 (Rfree = 0.000) for 3044 atoms. Found 13 (20 requested) and removed 23 (13 requested) atoms. Cycle 15: After refmac, R = 0.2649 (Rfree = 0.000) for 3031 atoms. Found 12 (19 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.86 2.53 Search for helices and strands: 0 residues in 0 chains, 3099 seeds are put forward Round 1: 310 peptides, 31 chains. Longest chain 31 peptides. Score 0.678 Round 2: 322 peptides, 24 chains. Longest chain 49 peptides. Score 0.753 Round 3: 331 peptides, 28 chains. Longest chain 49 peptides. Score 0.737 Round 4: 320 peptides, 27 chains. Longest chain 41 peptides. Score 0.728 Round 5: 325 peptides, 29 chains. Longest chain 32 peptides. Score 0.720 Taking the results from Round 2 Chains 28, Residues 298, Estimated correctness of the model 75.6 % 6 chains (132 residues) have been docked in sequence Building loops using Loopy2018 28 chains (298 residues) following loop building 6 chains (132 residues) in sequence following loop building ------------------------------------------------------ 9938 reflections ( 99.76 % complete ) and 5187 restraints for refining 3089 atoms. 3531 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2979 (Rfree = 0.000) for 3089 atoms. Found 19 (19 requested) and removed 38 (13 requested) atoms. Cycle 17: After refmac, R = 0.2870 (Rfree = 0.000) for 3057 atoms. Found 18 (18 requested) and removed 19 (13 requested) atoms. Cycle 18: After refmac, R = 0.2766 (Rfree = 0.000) for 3053 atoms. Found 10 (18 requested) and removed 13 (13 requested) atoms. Cycle 19: After refmac, R = 0.2737 (Rfree = 0.000) for 3041 atoms. Found 9 (17 requested) and removed 15 (13 requested) atoms. Cycle 20: After refmac, R = 0.2678 (Rfree = 0.000) for 3034 atoms. Found 9 (17 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.88 2.55 Search for helices and strands: 0 residues in 0 chains, 3130 seeds are put forward Round 1: 313 peptides, 32 chains. Longest chain 43 peptides. Score 0.675 Round 2: 321 peptides, 26 chains. Longest chain 40 peptides. Score 0.737 Round 3: 326 peptides, 28 chains. Longest chain 31 peptides. Score 0.730 Round 4: 334 peptides, 28 chains. Longest chain 37 peptides. Score 0.742 Round 5: 330 peptides, 28 chains. Longest chain 28 peptides. Score 0.736 Taking the results from Round 4 Chains 30, Residues 306, Estimated correctness of the model 73.6 % 7 chains (86 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 74 B and 77 B 29 chains (307 residues) following loop building 6 chains (88 residues) in sequence following loop building ------------------------------------------------------ 9938 reflections ( 99.76 % complete ) and 5622 restraints for refining 3089 atoms. 4186 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3170 (Rfree = 0.000) for 3089 atoms. Found 16 (16 requested) and removed 35 (13 requested) atoms. Cycle 22: After refmac, R = 0.2921 (Rfree = 0.000) for 3059 atoms. Found 16 (16 requested) and removed 16 (13 requested) atoms. Cycle 23: After refmac, R = 0.2814 (Rfree = 0.000) for 3053 atoms. Found 14 (15 requested) and removed 15 (13 requested) atoms. Cycle 24: After refmac, R = 0.2725 (Rfree = 0.000) for 3046 atoms. Found 8 (15 requested) and removed 16 (13 requested) atoms. Cycle 25: After refmac, R = 0.2692 (Rfree = 0.000) for 3033 atoms. Found 11 (14 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.86 2.53 Search for helices and strands: 0 residues in 0 chains, 3125 seeds are put forward Round 1: 305 peptides, 36 chains. Longest chain 26 peptides. Score 0.624 Round 2: 327 peptides, 27 chains. Longest chain 40 peptides. Score 0.739 Round 3: 332 peptides, 27 chains. Longest chain 37 peptides. Score 0.746 Round 4: 347 peptides, 30 chains. Longest chain 31 peptides. Score 0.747 Round 5: 324 peptides, 34 chains. Longest chain 25 peptides. Score 0.678 Taking the results from Round 4 Chains 37, Residues 317, Estimated correctness of the model 74.5 % 8 chains (122 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 B and 58 B 35 chains (320 residues) following loop building 7 chains (131 residues) in sequence following loop building ------------------------------------------------------ 9938 reflections ( 99.76 % complete ) and 5076 restraints for refining 3089 atoms. 3461 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3204 (Rfree = 0.000) for 3089 atoms. Found 13 (13 requested) and removed 41 (13 requested) atoms. Cycle 27: After refmac, R = 0.2952 (Rfree = 0.000) for 3052 atoms. Found 13 (13 requested) and removed 17 (13 requested) atoms. Cycle 28: After refmac, R = 0.2847 (Rfree = 0.000) for 3040 atoms. Found 13 (13 requested) and removed 15 (13 requested) atoms. Cycle 29: After refmac, R = 0.2759 (Rfree = 0.000) for 3034 atoms. Found 13 (13 requested) and removed 16 (13 requested) atoms. Cycle 30: After refmac, R = 0.2680 (Rfree = 0.000) for 3025 atoms. Found 8 (13 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.89 2.56 Search for helices and strands: 0 residues in 0 chains, 3142 seeds are put forward Round 1: 292 peptides, 37 chains. Longest chain 31 peptides. Score 0.587 Round 2: 299 peptides, 35 chains. Longest chain 26 peptides. Score 0.621 Round 3: 320 peptides, 32 chains. Longest chain 28 peptides. Score 0.688 Round 4: 320 peptides, 34 chains. Longest chain 33 peptides. Score 0.671 Round 5: 320 peptides, 32 chains. Longest chain 30 peptides. Score 0.688 Taking the results from Round 5 Chains 36, Residues 288, Estimated correctness of the model 62.6 % 4 chains (62 residues) have been docked in sequence ------------------------------------------------------ 9938 reflections ( 99.76 % complete ) and 5827 restraints for refining 3089 atoms. 4498 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3077 (Rfree = 0.000) for 3089 atoms. Found 13 (13 requested) and removed 30 (13 requested) atoms. Cycle 32: After refmac, R = 0.2877 (Rfree = 0.000) for 3061 atoms. Found 13 (13 requested) and removed 20 (13 requested) atoms. Cycle 33: After refmac, R = 0.2778 (Rfree = 0.000) for 3052 atoms. Found 13 (13 requested) and removed 18 (13 requested) atoms. Cycle 34: After refmac, R = 0.2722 (Rfree = 0.000) for 3044 atoms. Found 13 (13 requested) and removed 15 (13 requested) atoms. Cycle 35: After refmac, R = 0.2672 (Rfree = 0.000) for 3040 atoms. Found 10 (13 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.87 2.54 Search for helices and strands: 0 residues in 0 chains, 3145 seeds are put forward Round 1: 282 peptides, 32 chains. Longest chain 23 peptides. Score 0.614 Round 2: 294 peptides, 31 chains. Longest chain 29 peptides. Score 0.648 Round 3: 291 peptides, 28 chains. Longest chain 29 peptides. Score 0.669 Round 4: 287 peptides, 30 chains. Longest chain 27 peptides. Score 0.643 Round 5: 295 peptides, 31 chains. Longest chain 27 peptides. Score 0.650 Taking the results from Round 3 Chains 28, Residues 263, Estimated correctness of the model 58.3 % 6 chains (100 residues) have been docked in sequence ------------------------------------------------------ 9938 reflections ( 99.76 % complete ) and 5537 restraints for refining 3089 atoms. 4176 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2934 (Rfree = 0.000) for 3089 atoms. Found 13 (13 requested) and removed 34 (13 requested) atoms. Cycle 37: After refmac, R = 0.2765 (Rfree = 0.000) for 3057 atoms. Found 12 (13 requested) and removed 16 (13 requested) atoms. Cycle 38: After refmac, R = 0.2742 (Rfree = 0.000) for 3046 atoms. Found 8 (13 requested) and removed 13 (13 requested) atoms. Cycle 39: After refmac, R = 0.2669 (Rfree = 0.000) for 3040 atoms. Found 7 (13 requested) and removed 13 (13 requested) atoms. Cycle 40: After refmac, R = 0.2594 (Rfree = 0.000) for 3031 atoms. Found 10 (13 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.86 2.53 Search for helices and strands: 0 residues in 0 chains, 3116 seeds are put forward Round 1: 282 peptides, 37 chains. Longest chain 22 peptides. Score 0.564 Round 2: 292 peptides, 32 chains. Longest chain 28 peptides. Score 0.635 Round 3: 308 peptides, 28 chains. Longest chain 30 peptides. Score 0.700 Round 4: 310 peptides, 29 chains. Longest chain 30 peptides. Score 0.695 Round 5: 293 peptides, 29 chains. Longest chain 29 peptides. Score 0.664 Taking the results from Round 3 Chains 32, Residues 280, Estimated correctness of the model 65.2 % 5 chains (81 residues) have been docked in sequence ------------------------------------------------------ 9938 reflections ( 99.76 % complete ) and 5656 restraints for refining 3089 atoms. 4279 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2882 (Rfree = 0.000) for 3089 atoms. Found 13 (13 requested) and removed 24 (13 requested) atoms. Cycle 42: After refmac, R = 0.2748 (Rfree = 0.000) for 3070 atoms. Found 13 (13 requested) and removed 15 (13 requested) atoms. Cycle 43: After refmac, R = 0.2680 (Rfree = 0.000) for 3055 atoms. Found 12 (13 requested) and removed 13 (13 requested) atoms. Cycle 44: After refmac, R = 0.2640 (Rfree = 0.000) for 3050 atoms. Found 13 (13 requested) and removed 13 (13 requested) atoms. Cycle 45: After refmac, R = 0.2609 (Rfree = 0.000) for 3049 atoms. Found 7 (13 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.89 2.56 Search for helices and strands: 0 residues in 0 chains, 3158 seeds are put forward Round 1: 280 peptides, 42 chains. Longest chain 23 peptides. Score 0.506 Round 2: 297 peptides, 35 chains. Longest chain 29 peptides. Score 0.617 Round 3: 297 peptides, 33 chains. Longest chain 31 peptides. Score 0.636 Round 4: 276 peptides, 30 chains. Longest chain 25 peptides. Score 0.621 Round 5: 290 peptides, 33 chains. Longest chain 30 peptides. Score 0.621 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 264, Estimated correctness of the model 50.4 % 8 chains (75 residues) have been docked in sequence Sequence coverage is 28 % Consider running further cycles of model building using 1vra-3_warpNtrace.pdb as input Building loops using Loopy2018 36 chains (264 residues) following loop building 8 chains (75 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9938 reflections ( 99.76 % complete ) and 5847 restraints for refining 3089 atoms. 4583 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2936 (Rfree = 0.000) for 3089 atoms. Found 0 (13 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2877 (Rfree = 0.000) for 3069 atoms. Found 0 (13 requested) and removed 9 (13 requested) atoms. Cycle 48: After refmac, R = 0.2872 (Rfree = 0.000) for 3059 atoms. Found 0 (13 requested) and removed 3 (13 requested) atoms. Cycle 49: After refmac, R = 0.2793 (Rfree = 0.000) for 3053 atoms. TimeTaking 60.18